The ecology of estuarine channels of the Pacific Northwest coast: A ...

. ~ -~c-~*-ii"~.:~vT~FISH h VI:LT~L':": -.A December FWS/OBS-83/05 1983w~I..~-'stH- Sfidell CompYLe. COD"V~*~1010 cause f4auIev~rdSlidell, LA 70458NMATHE ECOLOGY OF ESTUARINE CHANNELSOF THE PACIFIC NORTHWEST COAST:A COMMUNITY PROFILEChar1 es A. SirnenstadFisheries Research InstituteColl ege of Ocean and Fishery SciencesUniversity of WashingtonSeattle, WA 98195Project OfficerJay F. WatsonU.S. Fish and Wildlife Service500 N.E. Mu1 tnomah StreetPortland, OR 97232Prepared forU.S.Department o

PREFACEThis profile of the estuarine channel habitats or subecosystems, considerabl ehabitats of the Pacific Northwest is one effort was dedicated to detailing hydro-in d series of conmuni ty profiles synthe- 1 ogical , geonorphological , and chemicalsizing information pertinent to specific components and processes of the systems ashdbitats of particular interest to envi- well as the biological. These factors inronmental managers. The intent of the concert with the biota dictate both theseries is to provide scientific infor- short- and long-term ecological structureoation in a format that is useful to a and function of these habitats. The finalbroad spectruin of users including envi- chapter integrates the information in therormentdl managers, col 1 ege educators, and preceding chapters by detail ing considerinterestedlaypersons. This specificprofile focuses or1 the cornpl ex network ofations for management.channels of various origins in the estu- Any questions or comments about orarine reaches of the coastal waters of the requests for pub1 ications shor~ld bePacif i c Pbrthwest. The geographic scope di rected to:or study area is primarily that region ofthe coast from Strait of Juan de Fuca onInformation Transfer Special istthe north to Cape Plendoci no, Cal ifornia, National Coastal Ecosystems Teamon the south. U.S. Fish and Wildlife ServiceNASA/Sl idel 1 Computer Conpl exIn order to explain the ecology with-1010 Gause Boul evardin these channel systetns and their Sl i dell , LA 70458ec1~1 ogical re1 ationships to the adjacenti i i

COr4VERSI ON FACTORSMetric to U.S.CustomaryTo Obtainmil 1 imeters (m)centimeters (cm)meters (m)ki1 ometers (km)2square meters (m )square ki 1 ometers (km )hectares (ha)liters (1)cubic meters (m3)cubic meters (m )milligrams (mg)grarns (g)kilograms (kg)metric tons (rat)metric tons (mt)ki l ocal ori es (kcal )Cel s ius degrees1.8(C0) t 32inchesinchesfeetmil essquare feetsquare milesacresgal 1 onscubic feetacre-feetouncesouncespoundspoundsshort tonsBTUFahrenheit degreesinchesinchesfeet (ft)fa thomsmiles (mi)nautical miles (mi)2square feet (ft )acres 2square miles (mi )gallons (gal)cubic feet (ft )acre- feetounces (oz)pounds (Ib)short tons (ton)BTUU.S.Customary to Metricmil 1 imeterscentimetersmetersmeterskilometerskil meterssquare metershectaressquare ki 1 ometers1 i terscubic meterscubic metersgramskil ogramsmetric tonski 1 ocal ori esCelsius degrees

CONTENTSPagePREFACE ............................. i iiCOPNERSION FACTORS ........................ ivLIST UF FIGURES ......................... viiiLIST OF TABLES .......................... xiACKNOWLEDGMENTS ......................... xiiCHAPTER 1 . 1NTRODUCTI.ON ..................... 11.1 Objectives ......................* 11.2 Scope ......................... 21.3 Methods ........................ 2CHAPTER 2 . PHYSICAL DESCRIPTION OF ESTUARINE CHANNELS ...... 42.1 DefinitionandDescription ............... 42.2 Geomorphol ogy ..................... 42.3 Circulation ...................... 102.4 Water Mass Characteristics ............... 122.4.1 Physical .................... 122.4.2 Chemi cal .................... 142.5 Substrate Characteristics ............... 182.5.1 Physical .................... 182.5.2 Chemical .................... 212.6 Itemization and Classification of EstuarineChannel Habitats in Region .............. 25CHAPTER 3 . PRIMARY PRODUCTION IN ESTUARINE CHANNELS ....... 323.1 Benthic Mi crof lora ................... 323.2 Macroalgae ....................... 323.3 Angiosperms ...................... 333.4 Phytoplankton ..................... 333.5 Estimates of Standing Crop and PrimaryProduction Rates ................... 343.6 Driving and Limiting Variables to PrirflaryProduction ...................... 35CHAPTER 4 . UETRITUS PROCESSING IN ESTUARINE CHANNELS ...... 384.1 Detritus Sources .................... 384.2 Distribution of Detritus ................ 414.3 Fungi and Bacteria Colonization ............ 424.4 Physical. Chemical. and Biological Conditioning .... 42

CHAPTER 5 . INVERTEBRATE ASSEMBLAGES OF ESTUARINE CHANNELS .... 465.1 Bentni c Infauna and Sessi 1 e €pi fauna .......... 465.2 Motile Epifauna .................... 525.3 Epibenthic Zooplankton ................. 545.4 Pel ayi c Zoopl ankton and Neuston ............ 62CHAPTER 6 . FISH ASSEMBLAGES OF ESTUARINE CHANNELS ........ 686.1 Demersal Fishes .................... 686.2 Pelagic Fishes ..................... 716.2.1 Resident Pelagic Fishes ............. 736.2.2 Anadromous Pelagic Fi shes ............ 786.2.3 Ichthyopl ankton ................. 86CHAPTER 7 . BIRD ASSEMBLAGES OF ESTUARINE CHANNELS ........ 877.1 Shallow-Probing and Surface-Searching Shorebirds .... 877.2 Waders ......................... 937.3 Surface and Diving Waterbirds ............. 947.4 Aerial -Searching Birds ................. 95CHAPTER 8 . MAMMALS OF ESTUARINE CHANNELS ............ 978.1 Terrestrial Mammal s .................. 998.2 Aquatic Mammals .................... 998.3 Marine Mammals ..................... 100CHAPTEK 9 . TRUPHIC AND COMMUNITY ECOLOGY OF ESTUARINECHANNELS ............................ 1039.1 Principal Pathways of Energy Flow throughInternal Food Webs .................. 1039.2 Roles of Predation and Competition Interactionsin Structuring Communities and Food Webs ....... 1129.3 Estuarine Channels as Critical Reproductive.Nursery. Foraging. and Refugia Habitats ....... 1139.4 Interrelationships among Estuarine ChannelHabitats and Riverine. Wetland. Oceanic. andOther Estuarine Habitats ............... 115........10.1 Sources and Mechanisms of Impact ............ 11910.2 Utilization of and Dependence on Channels by Economicaily-and Ecolopically-Important Species .... 124CHAPTEK 10 . SUMMARY . THE RULE OF CHANNEL HABITATS INESTUARINE ECUSYSTEMS AND MANAGEMENT IMPLICATIONS 117.......................10.3 Rates and Pathways of Recovery from Short-termImpacts 125v i

Page10.4 Methods of Channel Restoration andRehabilitation . . . . . . . . . . . . . . . . . . . . 12610.5 Research Gaps and Priorities . . . . . . . . . . . . . . 12710.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . 129LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . 130APPENDICES: A. Glossary of Terms . . . . . . . . . . . . . . . . 1598. Sediment Classification Schemes . . . . . . . , . 165C. Tidal Channel Characteristics f.leasurements. . . . 167D. Summary of Current Research andResearch Groups/Centers AddressingEstuarine Channel Ecology orEffects of Alteration of Channel Habitats . . . 175vii

Fi g.LIST OF FIGURESPage1.1 Location of estuaries in Oregon and Washington ....... 22.1 Kepresentati ve estuarine channel classesand geomorphologi es and associated estuari nefeatures and regions 5....................2.2 Example of estuarine channel habitats in Pacifickrthwest; (A) braided mainsten channels of main armof Fraser River are separated by saltmarsh habitat,and (B) closer view of bl ind channels in sal trnarshhabitat on Woodward Is1 and. ................. 62.3 Estuarine channel mouth depositional patternsassociated with macrotidal systems in the absence(A) and presence (6) of strong wave action ......... 82.4 Estuarine channel dimensional characteristics ........ 92.5 Estuarine classification diaorami 11 us tra ti ng seven types ofestuarine circulation .................... 112.6 Sediment size fraction (% wet weight) distributedat seven channel bottom and slope locations inGrays Harbor 20........................2.7 Volatile solids (% of total dcy weight) in sedimentsat seven channel bottom and slope locationsin Grays Harbor ....................... 232.8 Distribution of organic matter (volatile solids,chemi cal oxygen demand, and tota 1 organic carbon )in sediments at fourteen channel bottom and slope/bank locations in Grays Harbor 24...............3.1 Primary production compartments and driving variablesand limiting factors i nf fuenci ng distri bution,standing crop, and rate of production 36 .........tuarine channel habitats of thes t *.....................39e mechanisms and flowsmical, and biological................ 43

Fig.Page4.3 Terrestrial (wood chips, tree bark, and leaves)detritus of varying particle sizes deposited onlittoral flats of Duckabush River estuary, HoodCanal, Washington 43......................5.1 Representative illustration of common benthic infaunaand sessile epifauna assemblages of estuarinechannel habitats of the Pacific Northwest 49..........5.2 Representative illustration of common motile epifaunaassemblages of estuarine channels of thePaci f i c Northwest ...................... 555.3 Representative illustration of common epibenthiczooplankton assemblages of estuarine channel habitatsof the Pacific Northwest 57..................5.4 Representative illustration of common pelagic zoopranktonand neuston assemblages of estuarine channelsof the Pacific Northwest .................. 64....6.1 Kepresentative illustration of common fish assemblayesof estuarine channels of the Pacific Northwest 726.2 Mean Shannon-Weaver diversity index of demersalfishes in the Columbia River estuary as a functionof location along the longitudinal axis (A)and over the 18-month sampling period (B) .......... 726.3 Mean Shannon-Weaver diversity index of pel agicfishes in the Columbia River estuary as a functionof location along the longitudinal axis (A)and over the 18-month sampling period (B) 77..........6.4 Tidal channel trap net set in blind channel of FraserRiver estuary to sample juvenile salmon utilizingsal tmarsh habitat 82..........................7.1 Representative illustration of common bird assemblagesof estuarine channels of the Pacific Northwest 917.2 Representative avi fauna of estuarine channel habitatsin thepacific Northwest ................7.3 Seabird (primarily rhinoceros auklets, commarbled murrelets, and pigeon gui 1 lemots)ti on in Grays Harbor, Washington, OctoberSeptember 1975..............8.1 Representative illustration of commonblages of estuarine channels of the Pi x

Fig. -8.2 Pacific harbor seal haulout site along channel inWillapa Bay, Washington, June 1980 ............. 1018.3 Maximum total abundance of Pacific harbor sealsat haulout sites in three of Washington's coastalestuaries in 1980 and in 1981 ............... 1029.1 Representative food web of estuarine channel habitatsof the Pacific Northwest. 111..................10.1 Configuration of channel habitats in the Cot umbiaRiver estuary in 1868-1875 (A) and recent time (B). ..... 11810.2 Late 1800's dredging of Uuwamish River channels andlittoral flats in Elliott Bay, Seattle, Washington ..... 12010.3 Example of where diking and filling have removed(blind or tidal) channel habitat in Fraser Riverestuary: {A) i 1 lustrates diking of subsidiary(entering from lower right) channel and blindchannels in sal tmarsh and (B) shows historicalchannel patterns still evident in existing fields ...... 122

This synthesis of infomation onestuarine channel s of the Pacific Northwestwoul d have been virtual ly impossibl ewithout the aid and assistance of manyindividuals, to whom I extend my utrnostgratitude. John Cooper, Jay Watson,Nancy Nelson, and their coll eagues in theU.S. Fish and Wildlife Service were responsiblefor initiating and sustainingthe effort, providing reference material,and generating critical reviews. Robertdolton and Duane Higley (Oregon StateUniversity, Corvall is), David Levy (WestwaterResearch Centre, Vancouver, B. C. ),Colin Levings (Department of the Environment,Vancouver, B.C.), Ed Roy (Universityof Washington, Seattle), DennisPaul son (Uni vers i ty of Washington,Seattle), and Rocky Beach (Oregon Departmentof Fish and Wild1 ife, Astoria) allcontributed data, reports, ideas, andreview comments which were the crux ofthis synthesis. Independent reviewerswho a1 so provided extremely constructivecomr~ents included A1 yn Duxbury (University of 'rlashington, Seattle), Tom Gamer{Oregon Department of Fish and W i l dl ife,Hewport), and Char1 es Mil 1 er (OregonState University, Corvall is). The incrediblyfine it 1 ustrations were preparedby Cathy Eaton Walker of Friday Harbor,Washington. Appreciation is extended toDr. Dennis Yillows, Director of the University of Washington's Friday HarborLaboratories, for the opportunity to obtainoriginal aerial photographs ofestuarine channel s in Puget Sound. I arla1 so grateful for the photographs providedby Rocky Reach, Dave Levy, andDenni s Paul son.

This document has been prepared withthe objective of providing estuarine resourcemanagers with a synopsis of theexi sting knowledge about the ecology ofestuarine channels in the Pacific Northwest.Incorporated into this profile isa summary of the principal physical, chemicalenvironments and biological featuresof channel communities, as we1 1 as an interpretivesynthesis of the internal dynamicsof the community and its relationshipswith other communities in theaggregate estuarine ecosystem.And, while this community profile hasbeen specifically prepared to provideinformation for the assessment, planningand permitting activities of the U.S. Fishand Wildlife Service, it w i l l nopefullyconstitute an educational source documentfor all those interested in the ecologicalvalue of estuaries.STRAIT OFJUAN DE FUCASTRAIT OF GEORGIAQUINAULT RlVERGRAYS HARBORWILLAPA BAYCOLUMBIA RlVERNECANICUM RlVERNEHALEM BAYNETARTS BAYSAND LAKENESTUCCA BAYSALMON RlVERSILETZ BAYPORT MOODY ARMPUYALLUP RlVER1.2 SCOPEYAQUlNA BAYThe reg ion of geographic coverage SIUSLAW RlVER(Fig. 1.1) is the Columbian Province(Cowardin et al. 1979), including the UMPQUA RIVERNorthwest Pacific Coast from Cape Hendocino,California, to the Strait of Juan deFuca on the Washington-Canada border. COQUILLERIVERThis embraces coastal estuaries as wellas the continuum of estuaries forming theinland seas of Puyet Sound and the south- ROGUE RIVERern Strait of Georgia, with the latter PlsToLRIVERterminating between Vancouver on themain1 and and Nanaimo on Vancouver Is1 and.PT ST GEORGE -Ir/CALIFORNIAEstuarine channel habitats are definedas incised subtidal estuarine bot-TRINIDAD HEADtoms or depressions which contain saline(> 0.05~/,,) water masses freely exchangedt5rough tidal and riverine currents. Thisdefinition is intended to encompass boththe principal corridor of water movement Fig. 1.1. Location of estuaries in Oregonthrough the estuary, typically along its and Washington.main longitudinal axis, as well as thecornplex dendritic or anaStomosin9 drain- resident or transitional, in or on theayes which dissect tidefl atS and Salt- water column or subtidal substrate.marshes.The biotic community characterizing1.3 METHODSestuarine channels involves the micro- This community prof i 1 e was constructandmacroflora and fauna found, whether ed through a synthesis of the physioyra,-,2

phy, biota, ecoloyical interactions, andeffects ot human nlanipul ations in channelnabi tats of Pacific Northwest estuaries.Material was gathered from published aswell as unpublished reports and other"gray" literature, some of which are citedas examples of the processes being described.Unless 0therwi se cited, interpretationsand conclusions based upon unpublisneddata are sole11 those of theauthor.Reference sources of particular usein this synthesis included the U.S. Fishand Wi ldi 1 fe Service, Biological ServicesProgram's Ecological Characterization ofthe Pacific Northwest Region (Proctor etal. 1980) and Pacific Coast EcologicalInventory (Beccasio et dl. 1981).

2.1 DEFINITION AND DESCRIPTIONCYAPTER 2PHYSICAL DESCRIPTION OF ESTUARINE CHANNELSA1 though a diverse array of mor- occurs the principal transport of waterphol ogies characterize Pacific Northwest into and out of the estuary; subsidiarestuaries, a1 1 basi cdl ly meet the gener- (stream) channels through which mino;ally-accepted definition of Pritchard water transport occurs; and bl ind or tidal(1967), "An estuary is a semi-enclosed channels which primarily drain flats ofcoastal body of water which has a free tidally or flood-introduced water ratherconnection with the open sea and withinwhich sea water is measurably diluted withthan runoff from associated wet1 ands anduplands. Examples of several of thesefreshwater derived from land drainage." classes of channels are found in theBy this definition we exclude coastal Fraser River estuary (Fig. 2.2).lagoons, brackish seas, and sal ine lakeswhich have neither the dynamic tidal 2.2 GEOMORPHOLOGYexchange of sea water nor riverine inputof freshwater characterized by true es tu- Pri tchard (1967) and Russel 1 (1967)aries and where riverine input is typical- also classified four types of estuariesly exceeded by evaporation. In the PacificNorthwest, however, estuarine "systems"based upon their geological origin anddevel opnent: 1) drowned river vall eys,such as Puget Sound and the Strait of which were produced by rises in sea levelGeorgia also meet this definition of an or subsidence of land; 2) fjords, whereinestuary, but which, because of their deep, U-shaped estuaries were formed bypredominantlymarine nature, we will also glacial action; 3) bar-built estuaries,exclude in favor of addressing the srnallerestuaries found within them.created by accumulation of sedimentsacross an open rivermouth or coastalbight; and 4) estuaries resulting fromWithin an estuary, channels are tectonic processes such as faulting.defined as, "an open conduit either naturallyor artificially created which peri-There is also at least one case in thePacific Northwest of a fifth type ofodi cally or continuously contains moving estuary, that created by man-made mani puwater,or which forms a connecting link lations of river course and shorelinebetween two bodies of standing water" rnorphol ogy.(Langbein and Iseri 1960). As such,channels constitute critical interfaces Configurations of tidally influencedwithin the estuary itself, linking litto- deltas ~hich form intersections betweenral and sublittoral, riverine and marinehabitats. The wl ationship between estuestuarinechannels and the ocean aregoverned by sediment dispersal and accumuarinechannels and other components of the lation patterns. Wright and Colemanestuary are illustrated in Figure 2.1. (1973), Coleman and Wright (1975), andWithin this definition fall three basic Wright (1977) have suggested that thesecl asses of channels: mains tem channel s patterns are determined by the i nteraction(thalwegs of Proctor et a1 . 1980) wherein between outfl ow dispersion (including4

Fig. 2.2. Example of estuarine cb,annel habitats in the Pacific Northwest; A) braidedmainstem channels of main arm of Fraser River are separated by sal tmarsh habitat, andB) a closer view of blind channels in saitmarsh habitat on Woodward Island (Photographscourtesy of David Levy, Westwater Research Centre, University of British Columbia, Canada).

envi roniiients) , bidirectional currentscreate sand-fil led, funnel-shaped di stri b-utaries in which 1 inear tidal ridges haverep1 aced the distributary mouth bar (Fig.2.3A) ; where strong wave action i nterceptsthe river mouth, constricted or deflectedchannel s develop (Fig. 2.3B). Swift(1976) a1 so developed categories of "tidalinlet" tnorphologi es, including (1) overlap,(2) offset, and (3) symmetrical,which could be applied to Pacific Northwestestuaries. See Elliott (1978a and b)and Reineck and Singh (1980) for furtherdiscussion of delta and inlet structure.The structure of estuarine channelsreflects, in part, the origins and developmentof the estuary as governed by thedynariiic forces of riverine and tidalcomponents. Morphologies of channel susually ref1 ect the original riverbedshape and pattern in drowned river valleyswhile channels in bar-bui 1 t estuaries areoften ephemeral in location and form.Given the glacial formation of fjords,channels in these estuaries tend to bestable and re1 atively permanent. Thisvariation in stability is reflected infour basic channel configurations: 1)fixed channels, which were erosionallycreated, usually remain in the same locationand the bed is deepened over time; 2)braided channels, which are characterizedby many divisions into smaller branchesaround lenticular bars or is1 ands, withthe branches uniting at various downstreamlocations; 3) meandering channels, whichhave a simple, winding course that changessystematically over time; and 4) dendri ticchannels, which have irregular branches1 eading to a common channel.The principal characteristics of thechannel bank are its slope and substrate,which are not only correlated but are alsoaffected by the orientation and veloci tiesof the river and tidal currents at thatpoint. Bank slope can be classified intofour gradient c,l asses: 1) vertical ,90"-45"; 2) steep, 45"-30"; 3) moderate,30"-5"; and 4) shallow, 5"-0".Substrate can be defined as eitherconsolidated (combined or firm rock orsoil ) or unconsol idated (loose and di sas-sociated particles). Unconsol idatedsedinents can be classified on the basisof particle diameter as: 1) silt or clay,2) sand, 3) gravel, 4) cobble, and 5)boulder and [nay be further divided withinthese categories (Appendix B) . Furtherdiscussion of the sediment characteristicsof estuarine channels is presented inSection 2.5.One of the few detailed studies ofestuarine channel morphology was Levy andNorthcote's (1981) documentation of tidal(bl ind) channel characteristics in theFraser Ri ver Estuary. Twenty-two habitatcharacteristics were measured at 15 separateblind channels, most of which weredendri tic in character. The channels werefurther classified into four orders: 1)channels of large subtidal sloughs orreaches which never dewater at low tide;2) large channels which experience highvelocity tidal flows and usually do notdewater at low tide; 3) intertidal channelswhich branch off second order channelsor sloughs and usually dewater completelyat low tide; and 4) small intertidalchannels which branch off second orthird order channels and always dewater atlow tide. These and several other characteristicsmay be utilized to define mostbl i nd and subsi dary estuarine channels andsome may be applied to the characteristicsof mainstem channels (Fig. 2.4). AppendixC lists the measurements and the valueswhich Levy and Northcote (1981) obtainedfrom their characterization of tidalchannel habitats in the Fraser RiverEstuary; the major descriptors of channel~norphology indicated predominantly thirdorder channels with relatively uniformtotal depths (Dc; 2 = 1.75 +- 0.33 m),trough depths (Dt; 8.69 + 5.63 cm), andinouth widths (W 1 -t W ; 13.2 + 6.0 in) butmore variable total ?engths L ; 579.6 ?505.3 m), total area (At; 5,370.3 i5,143.1 mz), and refugia area (357.9 2648.4 m2). Their analyses of the relationshipbetween channel characteristicsand fish assemblage cornposi tion ii lustratedsome significant associations betweenparticular assemblages and channelcharacteristics, including channel morphology (see Section 6.2.2).

Fig, 2.3. Estuarine channel mouth depositional patterns associated with macrotidal systemsin the absence (A) and presence (5) of strong wave action (from Wright 1977).

TRANSVERSE SECTIONMeasurements: W1+W2 = width between tops of banks perpendicularto axis of channel (m)Ac = transverse area (m2)u and u; balk angles as measured by tan-l Dc/W1At= total area, typically meaz~.-ed byand tan-1 D,/WE. respectively; (')planimetry frm charts (m2)Channel Characteristics:Dc = total depth (m) total length = length of main axis channel (LC)and subchannels (1 (m)Dt = depth of trough in bottom of channelwhich usually carries residual tidalperimeter = wetted perimeter (P) of main axisflow (cm)channel and subchannel s; (m)Ei = elevation of channel bottm at gradient = drop in elevation (€?-El ) betweenmouth (m)mouth and end of channel, divided byE2= elevation of end of blind channel (m)axis length (LC); (m/m)E3 = elevation of surrounding bank (m)orientation = orientation of main axis from truenorth; (")H = height of surrounding vegetation;varies seasonally but typical lY meaaveragebank angle = mean of a and a ,; (")sured at peak production period; (m)angular deflection = angular deflection to pre-LC = axis length from mouth to furthest vailing flowing tide or river current;("1point on principal axis of channel (m)'1-5= lennth of subchannels (m)refugia area = area of watered pools remaining inchannel at low tide; (m2)Fig. 2.4. ~stuarine channel dimensional characteristics (adapted from Levy and Northcote1981).9

2.3 CIRCULATION mixed estuary; and 0 1 indicates awell-mixed estuary.Estuarine ci rculation is usuallydescribed in tenns of the role played by A further classification of estuariestidal currents relative to that of river proposed by Hansen (1965) and Hansen andflow and invol ves characterization of Rattray (1966) incorporates two dimension-water movements, mixing processes, and the 1 ess para~neters to describe the developdistributionof sal ini ty and temperature ment of stratification and gravitationalresul ting from these dynamic physical convection in estuaries. This approachprocesses. The nature of tidal cycles can utilizes stratification-ci rculation diaalsoinfluence estuarine circulation. In grams (Fig. 2.5) to describe a continuumthe Pacific Northwest, tides are purely of estuarine conditions where the ordinatediurnal or se~nidirunal for only a few days of the figure is the ratio of the tidalpermonth and are generally classified as averaged salinity difference between themixed (Thornson 1981). A traditional bottom and surface, 6s = sb-Ss, to thescheme of classification (Stommel and depth- and tidal-averaged sal ini ty (so) atFarmer 1952; Cameron and Pri tchard 1963; a given 'location, and the abscissa repre-Review by Bowden 1967) involves variations sents the ratio of the tidal-averaged netabout the simplest relationship between circulation velocity at the surface, US,river water and salt water, i.e., in the to the averaged, cross-sectional net riverabsence of other influences, the lower runoff flow velocity, Uf. This classifi-density river water will flow as a dis- cation scheme distinguishes seven types oftinct layer, separated by a discernibleinterface, over salt water. The principalestuaries:factors influencing this relationship Well-mixed estuaries;include fresh water flow, tidal currentsand resulting turbulence, the physical (11 type la, where the net flow is seadimensionsof the estuary, the Coriol is ward at all depths and upstreameffect. As a result, four types of estu- transfer of seawater is controlled byaries have been described around these diffusion and sal ini ty stratificationvariations: 1) salt wedge, which is is slight, andriver-flow dominated; 2) two-layer flow (2) type lb, the variation of type 1with entrainment, which is ri ver-flow where there is appreciable stratifi-dominated as modified by tidal currents;cation;3) two-layer flow with vertical mixing,which is a combined effect of river flow Partially-mixed estuaries;and tidal !nixing; and 4) verticallyhomogeneous, where tidal currents are the (3) type 2a, where net flow reverses atdominant physical process affecting circu-depth and both advection and diffulationand where the degree of mixing may sion are important determinants ofvary laterally. A number of cases excep- the flux of salt water upstream andstratification is slight, and(4) type 2b, the variant to type 2 wherestratification is prominent;Fjord estuaries;(5) type 3a, where advection dominates byaccounting for over 99% of the upstreamseawater transfer with 1 i ttlestratification, andthe mixing (6) type 3b, where the lower layer isdeep that the salinity gradient aassociated circulation are effectivly surface phenomenon; and,10

Sal t-wedge estuary;(7) where the archetypical stratificationis well developed.But as a result 3f extremes in stratificationin the upper vs. lower reaches ofdn estuary and in river discharge, theestuaries can actual Iy span several cl assifications,as indicated by the linesconnecti rly or extendi ng the various sarnpl epoitits in Fig. 2.5. Using this scheme,Harisen and Rattray (1966) compared theColumbia River estuary (drowned rivervalley) with the Strait of Juan de Fuca(fjord). They illustrated that the ColumbiaZiver estuary actually shifted from atype lh to a type 2b in response to decreasirigriver flow while the Strait ofJuari de Fuca fell into a type 3a estuary.They also included four other estuariesfor coinparison (Fig. 2.5). CH2M-Hi1 1(1931) also indicated that five sites inW i l lapa Harbor (also included in Fig. 2.5)sar~iple during June fell within or betweentype 3a and 3b. Classifications of someof the laryer estuaries have been assignedit1 Section 2.6.The configuration of the mouth of theestuary can have a marked effect on thedynarnics of tidal circulation through theestuary. Goodwin et al.'s (1970) tidalarialysi s of three Oregon coas ta1 estuariesindicated that the Inore constrictedentrances to A1 sea and Siletz Bays produced"choking" of tidal amplitude andtrurlcation of tidal amplification at theentrance to the estuary ~hich was notevident in Yaquina Bay. Tidal cq~rrentsalso tended to reach 9igher maxima in thecor\stricted, "choked" estuaries (over 2 msec-1 in Si letz Bay, 1 rn sec-' in A1 seaBay, and 0.6 rn sec-I in Yaquina Bay).Phase shifts between tidal elevations andtidal currents of 90" to 100' and thetemporal distribution of tidal amp1 ificationthrough the three estuaries alsoindicated the presence of (progressive)ref1 ected or resonating waves.One diinensi ona1 , vertical ly-i ntegratedmodels of circulation in the FraserRiver estuary (Crookshank 1971; Ages 1979)have been utilized to document the inter-active effect of tides and river dischargeupon water surface elevations. Theyi 1 lustrate that river discharge contributesprogressively lrlore to the rise andfall of water surface elevation at pointsfurther up (upriver) the estuary and that,as discharge increases, the point wherethe daily tidal fluctuations (rise andfa11 of water) cease to exist moves downthe estuary. One of the more interestingsimulated characteristics of that estuarywas a significant time lag between theupriver propagation of the flood and ebbtides (e.g., ebb tide taking two hours tomove the same distance that the floodmoved in one hour).Few studies have compared or classifiedcirculation among different classesof estuarine channels or within channelsystems. Officer (1976) provides the mostdetdiled and quantitative information todate. While many of the above schemes canbe applied broadly to estuarine channels,there are a nu~nber of factors, such as~inds, basin (bottom) and channel bathyinetry,and coastal storm surges, each ofwhich may become more important in affectingcirculation patterns on the smallscale. For exainple, Pethick (1980) indicatedthat shallow water asyrninetric tidesare respons i bl e for vel oci ty asymnietry anddendritic channel ~norphology is responsiblefor the position and strength ofvelocity surges within tidal channels.2.4 WATER MASS CHARACTER1 ST1 CS2.4.1 PhysicalPhysical characteristics of the watermasses occupying estuarine channels exh ibitbroad spatial and temporal variationdue to the flux and rnixing of differentwater masses over short-term (i.e.,tidal),intervediate (i.e.,storm event), andlong-term (i.e.,seasonal cycles) . Whilesome features of any one water mass may berelatively predictable, e.g., tidal volume,the synergistic interactions amongriverine, marine, and ambient estuarinewater masses and meteorologi cal eventscredte basically stochastic (random)patterns of water volume, velocity, ternperature,sediment content (turbidity),

and density over time. The variation ofthese parameters also changss kvith physicallocation in the estuary in response tothe proportional representation of thethree basic water masses and basin configuration.Total water volume of an estuarygenerally depends upon riverine runoff andtidal influx. Runoff volume depends uponprecipitation regimes and the drainagebasin of the rivers and tributaries to theestuary. Given the range in size ofdra.inage bas ins contributing to PacificNorthwest estuaries, from 6.68 x 105 km2for the Columbia River to less than 20 km2for Inany small estuaries along the coast,the range in average annual dischargevolume is correspondingly high; from over7,600 m3 sec-1 for the Columbia River toless than 20 m3 sec-1 for small streams,respectively. Short-term fluctuations,however, may be very dra~nati c, especiallyduring winter storm events. For example,short duration winter stom freshets inthe Columbia River can actually exceed theannual sustained summer freshet of over14,000 m3 sec-1 (Fox 1981). Flushingtirnes, in terms of the number of tidalcycles requi red to rep1 ace the estuary'svolume, vary as a function of river dischargeand coastal upwelling (Duxbury1979). Sum:ner flushing times for sevencoastal estuaries, summari zed by Johnsonand Gonor (1982), vary between 4 to 5tidal cycles (Salmon and Netarts Riversestuaries) compared to 63-68 tidal cycles(Coos Bay). Neal (1965) estimated flushingtimes for the Columbia River estuaryto be between two and ten tidal cycles.Pearson and Gotaas (1951), Call away(1965), and Stein and Denison (1965)estimated average flushing times for GraysHarbor of between 5 and 48 days ( 10 and 96tidal cycles) depending upon river flowvalues. Using a water mass budgetapproach, Duxbury (1979) estimated monthlyreplacement rates of between 20% (June)and 16G% (January) day-1 and correspondingresidence tirnes of 5.0 and 0.60 days,respectively, for inner (upper) GraysHarbor estuary. Flushing tirnes of coas ta1estuaries in the Pacific Northwest, however,may be highly variable dependingupon nearshore ocean conditions. InWillapa Bay a strong northwesterly windduring the summer can bring upwelled waterinto the bay from the ocean, promotingrapid flushing. At other times the ColumbiaRiver plume nay essentially block theturnover of bay and ocean water :nasses,and complete flushing at such tirnes couldtake more than 20 days (U.S. Army Corps ofEngineers 1976). Flushing times ofwithin-channel water masses have not beenaddressed, but, given the fact that mostof the transport occurs through thesechannels, we might safely assume that theyare somewhat shorter than those of theestuary as a who1 e.Temperature reg iines in es tua ri nechannels reflect the influence of bothexogenous riveri ne and mari ne water massesas well as endogenous estuarine waternasses transported off subl i ttoral and1 ittoral flats. Mixing of these threewater masses vi thin the channel habitatcreates a temperature structure whichvaries in a conservative manner accordingto the relative contribution of each waterInass. Marine waters represent the leastvariable temperature source. There isonly a narrow seasonal range between 3°Cand approxinately 17.0°C depending uponthe presence and extent of codstal upwelling(FlcGary 1971; Oregon State University1971; Proctor et al. 1980) and the influenceof riverine plumes from major sourcessuch as the Columbid (McGary 1971), Fraser(Waldichuck 1957; Tabata 1972), and Skagi tRivers (Cannon 1978). River temperaturestend to exhibit a greater temperaturerange over time, ranging from 0°C to over25°C depending upon air temperature, precipitation,solar incidence and snow/glacia1runoff. The waters in an estuary'schannels are derived ul timately fromexogenous sources which are entrained over1 ittoral and upper subl i ttoral flat habitatsduring flood tide cycles and riverineflood events. Heating or caoling of theflats prior to and during the period ofinundation can result in rapid and extremeelevation or depression of ambient watermass temperatures .The result of the dynamic mixing ofthese water masses within the channelsreduces the temperature extremes but sti 11

allows cons i derable short-term (within 2.4-2 .wedtidal cycles) variation. Temperatures inchannel Qabi tats in the Columbia River Estuarine mixing of the highly variestuaryrange between 5°C and 25°C (Park able coricentrations of dissolved salts andet al. 1972); 5°C and 20°C in Grays Harbor compositions of dissolved material charac-(Loehr and Co'llias 1981); and 4°C and 23°C teristic of river waters with the relainthe Duwamish giver estuary (Lenarz tively uniform chemical co~nposition of1969). Tidal effects caused temperatures coastal sea water produces a characteri s-in the Salnlon River estuary to fluctuate tic (nixing series between dilute andfrom 7.3"C due to the presence of rnarine saline end-members (~urton and Liss 1976).water on incoming spring tides to 18.Z°C Composition of river waters is influencedon outgoing tides \then river water was by precipitation and rock and soil weathpresent(Johnson and Gonor 1982). Fine- ering. As a result, considerable variaresolutionsalnpl ing of t~nperature and tion occurs as a result of the geologicalsalinity at one station in the Salmon character of the drainage area and differ-River estuary through a c01nplet.e tidal ences in the proportional contribution ofcycle (Johnson and Gonor 1982) illustrated ground water flow and surface runoffthdt the temperature of the water mass (Livingstone 1963; Gibbs 1970). In genermeasuredlate in the ebb tide originated al, calcium, bicarbonate, and silicate arein d low salinity water mass frorn at least usually the major dissolved constituents3 la;) up the es tuary. in river waters, while sodium, magnesium,chloride and sul fate predominate in seawater. In that sea water salts compriseSedilnent is transported into or ap;~roxirnately 282 of the dissolved materithroughthe estuary in suspension or in a1 at 5°/,0 salinity, the chemical compoboundarylayer flow along the bottom as sition of seawater predominates early inbed load. Accordingly, sirdilrient load and estuarine mixing processes (Burton andthe sources of the scdi~nent within the Liss 1976).estuarine channel vary seasonal ly withrjver discharge arid tidal flux (Boggs and This relationship was best illus-Jones 1976; Scheidegyer and PhippS 1976). trated for the Columbia River estuary(Park et a1 . 1972) , where Si02 (250-0 u ?I),02 (6.5-0.5 ml L-1) and winter NO3 (35-0Suspended sediitlent is; composed prin- I~M) could be attributed to river sourcescipally of sand and finer particles and r~hile PO4 (2.0-0 EM), total CO (2.0-1.0varies with water depth and velocity. uM), alkalinity (2.0-1.0 meq $-1 ), andSuspended sedi~llents in the Columbia River surmner NO3 values (20-0 uM) originatedabove the estuary consist of particles ~ 6 3 principally from oceanic water masses. AIn in diameter and the total suspended load recent review of historical water qua1 i tyinto the estuary, which can vary three- datd in the Columbia River estuary (Paciffoldfro111 year to year was estimated to ic Northwest River Basins Commission 1980)be 9.5 x 106 tons yr-I (Haushild et al. indicated considerable seasonal variation1966). suspended sedi:nent concentrations in nutrient concentrations a1 though nutri -can vary from 13-0 to 38.5 m L - ~ at the ent patterns had changed little over thesurface, 12.5 to 69.6 mg L' 9 within the last 20 years. Representative surnlnersalt wedge and 12.5 to 59.9 m~ L-l 1 m nutrient values were 0.002 rng L-1 PO4-P,above the bottom, depending upon location undetectable nitrate, and 4.0 mg L-1in the estuary, tidal stage, and current Si02 in riverine portions of the estuaryvelocity (university of Washinqton Depart- and 0.070 mg L-1 p04-P, 0.20 mg L-1 NO3-Nnlent of oceanography 1980). Total mean and 2.0 mg L-1 sio2 in marine regions; thesediment flux in drainage channels in the data suggested nitrate and phosphatelower estuary in February 1980 ranged depletion occurs within the estuary duringbetween 0.2 and 1.0 mg an-2 set-1 at late sulnlner a1 though coastal upwelling mayChinook and Sand Island and between 0.1 increase nutrient levels (NOg, PO4) in theand 0.7 mg tin-2 S~C-1 at f lwaco,lower estuary during the summer (Haertel14

et al. 1969; Oregon State Univ. School ofOceanography 1980b). In coinpari son,spring and surnlner values of NO3-N andtotal PO4-P in the Grays Harbor estuaryranged between 0.018 arid 0.055 mg L-I and0.003 and 0.060 mg L-1, respectively(Herman 1975).A1 though it is probable that nutrientinputs i nto es tuari ne channel habitats areartificially elevated during periods ofhigh river discharge due to runoff ofnitrogen and phosphorus from agricultureand silvicul ture-appl ied fertil izers inthe watershed, no causal data is avail ablefor Pacific Northwest estuaries. Coll iasand Lincoln (1977), however, calculatedthat the average inflow of phosphate intothe main basin of Puget Sourid was 1,223metric tons and the contribution of phosphatefrom all sewers was 12.6 rlletrictons, co~npared to 18,400 inetric tons ofphosphate in the main basin at any giver1time.Sa1 ini ty has traditionally beer1employed as an index of mixing, a1 thouglithis has been criticized because thedefinition of sal i ni ty depends upon theessenti a1 constancy of the re1 ati ve proportionsof the dissolved ions in seawater and the introduction of river watercauses departures frorn the nearly constantionic ratios of oceanic waters (Burton andLiss 1976). As indices of mixing, chlorinity, chlorosi ty or isotopic oxygenratio (180/169) values have also beensuyges ted as sui tab1 e paraineters (Boy1 e etal. 1974), but of these only chlorinityhas been r~easured frequently in estuarinechannels of the Pacific Northwest. Consideringthat our primary concern in thissynthesis is the biological structure anddynamics of estuarine channel communities,the spatial and temporal distribution ofsalinity structure in the estuary is anappropriate indication of the major chemi -cal factors structuring these com~nuni ties(Caspers 1967).Saline oceanic water is transportedinto an estuary by both advection anddiffusion (Bowden 1967). Advected oceanicwater masses are general ly referred to asthe " sal t wedge" a1 though diffusion pro-cesses can cause the intrusion of salinewater beyond the upstrearn 1 i~ni t of thesalt wedge. In such estuaries as theColumbia River, it appears that longi tuditialsalt transport via diffusion may besignificant (Hansen 1965; Hughes 1968;Dyer 1973; Hughes and Rattray 1980; Fox1981). 5al ini ty gradients can be distinctand sharp in situations where fresh andsaline water masses are stratified, orbroad and variable where vertical mixingpredoininates. Thus, tfie degree of bothsalinity intrusion and stratification isdependent upon es tuary inorphol ogy, riverdischarge, seni-diurnal and spri ng-neaptidal cycles, and short-term, stochasticevents such as storms; in terins of estuarymorphology, the rate of change of crosssectionalarea through the estuary and thebed topography are important factorsdetermining sal ini ty distribution (Prandl e1951).A1 though most silnul ation models ofestuarine circulation, such as thoseproduced for the Fraser River estuary(Crookshank 1971; Ages and Wool lard 1976),are vertically integrated (or, at best,integrate over two depth sectors), accuratedescriptions of current flow musttake into account the dynamic effect ofsal ini ty intrusion upon currents. Detailedempirical studies are requiredbefore more complex models can be assembled.Such field documentation in theFraser (Ages 1975) has illustrated therole of the salt wedye in modifying thetidal effect upon surface outflow. Inthis instance, the sa1 t wedge continuesits upstrearr) rrlotion after flood slack,then retreats down the estuary but maintainsits shape until it is finally carried out as a homogeneous water mass. Inthe Columbia Ri ver estuary, sal ine watercan be detected as far as 42 km upriverunder the combination of extremely lowriver discharge and neap flood tides, butonly as far as 10 km under high riverdischarge, with stratification more pronouncedduring neap tidal cycles thanspring tidal cycle (Hansen 1965; Dyer1973; McConnell et a1 . 1979; Jay 1981; Fox1981). It should be noted, however, thatthe archetypical salt wedge is not yenerallyfound in the Columbia River estuary

(D. Jay, Univ. Wash., pers. comm.).Loehr and Coll ias (1981) indicatedthat the extent of salinity intrusioti inGrays Harbor in June and July 1966 (riverflows, 49.1 m3s-1 and 68.4 m3s-1, respectively)varied according to the range oftidal cycle (i.e., neap vs. spring). Theextent of intrlrsion shifted four milesover the tidal cycle during a neap andless than a mile during a- spring tidalcycle. Simenstad and Egyers (1981) indicated that sal ini ties in channel habitatsbetween March and October 1980 were relativelyuniform (well mixed) in the centralportion of the estuary (Cow Point, +loonIsland), but typically stratified at theupper (Cosmo?ol is) and 1 ower (Stearn'sBluff) extremes of mixing zone. Sal initiesat the latter two sites ranged widelybetween 5"/,, and 25"/,, but covered anarrower range hetween 25"/,, and 36O/,,at tile site (Wes tport) near the mouth ofthe estuary.Salinity ranges at three channelsites (RM 1.0, 2.2 and 3.7) in Yaquina Baybetwwen 1960 and 1973 were 11.7°/00 (34.1-22.4'/,,; ~i = 29.7"/,,) at the lower endof the estuary, and 16.3"/,, (34.1-17.8"/,,; S; = 28.2"/,,) and 24.1°/,,(33.5-9.4"/,,; Si = 27.3"/,,) further upthe estuary (U.S. Army Corps of Engineers1975).Levy and Levings (1978) documentationof surface salinity at a channel in theSquamish River estuary a1 so indicated thebrodd seasonal fluctuations which canexist at one site. The maxima of 26-27"/,, occurred in the winter and lessthan 4O/,, sustained during the spring andsumrner ~nonths . This seasonal effect wasalso illustrated for a blind, dendriticchannel habitat in the Fraser River estuary(Kistritz and Yesaki 1979), wherewater flooding the channel and :narsh wasbrackish (3-8°/0,) only during high wintertides, despite the greater tidal rangedurin the summer (%5 m) than the winter(1.3 m3.River waters are typically moreacidic than sea water but pH gradients inestuarine channel s are a1 so affectedsignificantly by variations in the chemi -cal composition of the mixing watermasses. pH values in the Columbia Riverestuary range from 5.8 to 8.3 but usuallyfall between 7.6 and 7.9 within the mixingzone; tributary channel waters in the areaof Youngs Bay have been reported to beslightly more acidic than main channelwater in the adjacent estuary (Park et al.1980; Pacific Northwest River BasinsCofl~nission 1980). Herrman (1975) documentedspring-summer pH values between6.94 and 7.25 in the upper Grays iiarhorestuary, with the surface waters usudlly0.08 pH units less than the more salinebottom waters. A 13-year water qua1 itydata base for Yaquina Bay (U.S. Army Corpsof Engineers 1975), however, illustratedquite uniform pH values at three locationsthrough the estuary (at river miles 1.0,2.2 and 3.7), with ranges between 7.6 and8.6 (pH ji = 3.1 at all three locations).Dissolved oxygen (DO), in addition tobeing the essenti a1 el ernent in aerobicinetabolism by aquatic organisms, is involvedin the biochemical breakdown oforganic matter in marine environments. Inessence, aquatic organism are constantlycompeting for free dissolved oxygen andwill incur physiological limitations whendissolved oxygen 1 eve1 s decrease be1 owapproxirnately 5 pprn; the tolerance todepressed dissolved oxygen is highlyvariabl e among aqua tic organi sas, however,and many natural ly divergent structures ofmarine water colurnn and benthic communitiesare due to different dissolvedoxygen regimes.Due to [nixing of ri verine and marinewater masses and their typical rapid fluxthrough the habitat, estuarine channelstypical ly do not experience dissolvedoxygen depletion except during situationsof seasonal minima in water exchange ordue to increased organic loadings byorganic pollutants.Dissolved oxygen is considered to beprincipal ty regulated by: 1) the rate ofaddition of biological oxygen demand(BOD); 2) the net rate of addition orremoval of oxygen by benthic oxygendemand, photosynthesis, and respiration;

3) the rate of reaeration; and 4) the rateof removal of BOD by sedi:nentation orabsorption (Dobbins 1954). Longi tudi naldispersion, the rate at which a materialis dispersed by eddies and diffusion, isnot usually a significant factor in lacustrineand strea~n systems but is thought tobe riiore important in estuarine channel s .Gunnerson (1966, 1967) and Thornann (1957)provide evidence that patterns of dissolvedoxygen concentration in estuariesmay be highly periodic, potentially exhibiting annual, 14-day, 24-hour, and 12-hourcycles with the low frequency effectsbeing re1 atively more irnportant than thoseattributable to high-frequency phenomena.These cycles could be reasonably correlatedto daily and spring-neap tide variations,solar radiation intensity, andphotosynthesis.Lenarz's (1969) detailed analysis ofwater quality data from the Duwamish Riverestuary indicated that the 1 owes t concentrationof dissolved oxygen in the channelprobably was associated wit:? the upstreamedge of the salt wedge. Streamflow waspos i tively correlated to dissolved oxygenconcentration and this relationship wasattributed to increased turbulence (diffusion),lower retention time, and greaterdilution of BOD with increased streamflow.The timing of algal blooms, which oftenincreased dissolved oxygen concentrationsdramati call y, were a1 so determined to berelated to strearnflow and tidal prism.Dissolved oxygen level s in estuarinechannel s of the Paci fic Northwest arenaturally high, being at or near saturation,except in a few highly developedestuaries with high BOD loadings. TheColumbi a River estuary represents thePacific Northwest coast' s largest systemre1 ative to natural dissolved oxygenconcentration. Most estuarine waters areusual ly supersaturated (8-6 mg duringspring and summer inonths- and slightlyundersaturated (

several periods in the summer; the lowestvalues, 3 to 4 el!, L-I, were associatedwith the upstream edge (bottom) of thesalt wedye.Bi ocherni cal oxygen demand has notbeen as widely reported as dissolved oxygen.Five-day BOD levels in Yaquina Bayaveraged 1.2 mg L-1 tnrouyhout the estuaryand a maxima ot 6.6 my L-1 was recordedw~thin two miles of the trlouth (U.S.Army Corps ot Enyineers 1975). Surriinervalues in tirays Harbor ranyed between1.45 to 5.13 my L - ~ (Herrman 1975).2.5 SUBSTKATE CHARACTERISTICS2.5.1 PhysicalChannelsubstrates reflect both his-toric and extant conditions. The yeoloyi -cdl history of the estuary and its watersheddetermines the characteristics ofthe material tnrouyh which the channel 1sbeiny cut and of the sediment load borneby riverine currents. Uynarrlic hydroloyi -cal , tidal, and meteroloyical forces,however, affect the coinplex eroslon anddeposi t ion processes which are constantlystructuriny the channel. The reader isreferred to Elliott (1978a & b) and Keineckand Sinyh (1980) for rriore detaileddiscussions of sedimentation processes.trosiori can occur throuyh corrosion(chemical ) , corrasion (mechanical ), andcavitation (Morisawa 1968), aided by thesuckiny, liftiny forces of vortex action(Matthes 1947). Under vortex action loosenedmaterials are sucked upward and downstreasiwith tne vortex current. Localdiscontinuities or separations of flow occurwhere there is a change in current directionand velocity caused by obstaclesor impingeelent on channel walls. Theresult is a nonunifor111 distribution ofenergy at that point, which produces aveering and overturniny of water rnassesas spiral flow. Water velocity, size otobstructions, spacing and size of obstaclesand the sharpness of channel bendsdictate the amount of separation, turbulence,and vortex action.Besides yrowing deeper or cuttinynew beds, channels a1 so widen by lateralcorrasion and weathering of the wall sduriny hiyh water flow, which includestidal influxes. 80th channel cutting andwidening are inediated by the resistanceof the bed material. The critical erosionvelocity of unconsol idated materi a1varies as a function of the grain size.Hjul strom (1935) indicated velocity decreasedfrom ~200-500 cm sec-1 (~4-1Uknots) for particles 1 pm dia. to ~20-50cm sec-1 (Q0.4-1.0 knots) for particlesbetween 100 pm and 1 mm, and increased to500 cm sec-I ( Q:O knots) for particlesas large as 100 iilm dia. As a result,erosion of sand requires lower velocitiesthan of either silt or gravel. Sternbery(1967) estimated that the critical drayvelocity required to initiate generalsediment motion in a Puget Sound channelwas 2.2 cm sec-1 for sediment yrain sizesbetween 0.3 to 1.1 riim dia.Particles entrained and transportedby a water mass are deposited when thecurrent is no longer sufficient to carrythem either as suspended particles (sedimentload) or as bottom transported (bedload) particles. Deposition of the sedimentload occurs with loss of competencecaused by a decline in gradient, a reductionin velocity or a decrease in volume.Settliny velocities range trom 0.1 cmsec-I (0.~02 knot) for particles Q 20-30Dm dia. to Q100-3UU cm sec-1 (~1-6 knots)for particles 2-10 cm dia. (Hjulstrom1935; Sundborg 1956). These re1 ationshipsvary as a function ot the characteristicsof the particle (e.y., specific gravity)and water lrlass (e.y., salinity).Thus, the dynamic changes in velocity,direction, sediment load and densityot water rnasses moving throuyh estuarinechannels results in spatially and temporally variable sediment structure throuyhthe estuary, and with considerable variabi1 i ty arnong estuaries. A particularlyprominent feature to most estuaries is azone of minimum sediment particle sizewhich typically occurs within the "mix-i ny ," "entrapment ," "turbidity maximum,"or "null" zone where upstream bottom tidalcurrents approximately balance down-

stream river currerits (Arthur and tiall1979; Ll oern 1979). Maxin1u111 settl iny ofsuspended particles occurs within tniszone duriny slack water, but 111uch isresuspended duriny tl ood or ebb currents.The rrlixiny of riverirle arla sa i ine watermasses also results in the tlocculationot fine particles, both sediment (clay)and orydnic detritus, and these aggreyatessettle within this entrdpl~~ent zone.Hubl~el 1 and Cil enn (1973) docu~llentedtnat the mean size of channel sedilllent inthe Col urribia River estuary became proyressively finer downstrearrl tlirouyh thefl uvial and transitional regions, only tobecorne coarser in the marine reyion ofthe estuary. This relationship was verifiedin the rirore detailed CREDDP~ studiesof the Columbia Kiver estuary. The sedimentparticles in the rlrai n channel wereshown to decrease in modal size fro111 500-3UU 1,111 (1.01)-1.754) oft Grays Uay to 3UO-175 1 rn (1.75- 2.5114) oft Baker Uay (Royet al. 1979; University ot Washinyton Uepartrrlentof Oceanoyrapny 1980). Variationin channel sedi~nent structure, however, iswidely apparent and can be related to thecurrent speed and the extent of cornmunicationwith riverine or tidal flow (Universityof Washinyton Uepartment of Uceanography1980). Sedin~ents in channels witnopen corr~munication with the ColurribiaKiver, one of the estuary's rllajor tributaries,or the density-driven flow fromthe ocean, tend to be coarser than sedimentson adjacent sub1 ittoral or 1 ittoralflats. Where water flow is restricted toonly one end of the channel the sedimentyrain size is usual ly finer than on theadjacent flats. Channel bathymetrj !naya1 so affect these relationships, as finegrainedsedin~er~ts may also be found indeep segments of larye channels wherethere are low velocity water areas belowchannel sill depths.These re1 ationshi ps between sedirrlerltstructure and chanr?el ~norphof oyy have alsobeen i l 1 ustrated within Coos Bay, whereHancock et al. (1980) il lustrated thatsedi~lient yrain size remained relativelyconstant (250 v111) w itni n the Coos navi yationchdnnel but was an order of ~naynitudetiner (b2 ~111) in Isthmus Slouyh,which does not have significant freshwater current flow through the channel.[)ifferential distribution of sedimentcori~position is a1 so we1 1 ill ustratedin Phipps and ~cnernrer's (1980) data torthe hottorr~s drld slopes of the Grays tiarbornavi yation chdnnel (Fi g . 2.6). Gravel andcoarse particles tronl ri verine sourcestended to be distributed in the hiyhestand lowest reaches of the estuary, indicatinyboth riverine arid marine sources.Silts and clays accumulated within thernixiny zone, probably lrlore the result offlocculation processes than of settl iny.Fines (predori~i nantly sand) con~posed rnostof sedin~ents in the lower estuary andprobably represented sett 1 i ny f ronl bothriverine and estuarine water nlasses. Theprincipal di tference between bottom andslope habitats was the lonyitudinal positionof the peak occurrence of yravel,which was lower in the estuary in thechannel bottom sediments. This probablyreflected the niyher current velocitiesalony the bottom ot the channel.Sediments in the mainstem channel ofYaquina Bay tal l into three realnls ofdeposition (Kulm and Byrne 1967). TheIliarine redlm, extending 3 k~rl into tileestuary from its mouth, contains well-sorted, subangular to subrounded, fine tomedium sana. Tne marine-tluviati lerealrr~, occurring between 3 k~rr dnd 1U ~IIIfrorn the mouth of the estuary, has sedirr~entswith a wide ranye In texture, tromwell- to poorly-sorted, anyular to sub-rounded silt to isediurn Sdnd. Tne tluviatilerealm in the upper reaches of theestuary turther than 10 kln frorn the rnouttlis characterized by sedirl~ents which arepoorly sorted, anyul ar to subdnyu l aryrains 9f S i l t to codrse sand. Lrainsize in the lower 10 kt11 ot the estuaryaverayes 217 bm (150-291 urn) and 279 Llrnin the channel above 10 krn.Tne only comprehensive study of sub-2 ~ ~ , ~j~~~ ~ ~ ~ b i ~ ~ Oata t Develop- ~ ~ sidiary ~ and y blind estuarine channels inment Program.the region, that of the Westwater Research

CHANNEL BOTTOMC)CHANNEL SLOPEII,I/p GRAVELSTATION LOCATION(X wet wein Grays Hadistributed at seven

Centre, University of British Columbiastudies in the t-raser River estuary, describedsediments trom the center trouyhsof dendritic channels at Woodward andBarber Islands and Ladner Marsh as beingsandy, with the yrain size ranging between75 m and 192 In (Levy and Northcote1981). Sn~ith's (1980a) studies innorthern Puyet Sound indicated sedimentsfrom a dendritic channel alony the deltaof the North Fork Skagit Kiver were cornposedpredominantly of sand (81.13% byweiyht) and silt (lk1.322)~ with mednyrain size of 97.4 urn (3.36 @ ). Sedimentsfroin the bank (t 1.0 m elevationMLLW) of a principal tidal channel awayfro~rl the delta were coarser (229.2 urnC2.13 $1) and sandier (89.88%)) and had ayreater sand to mud ratio (8.88) than didthe sample from the dendritic channel onthe face of the delta (3.36).Bed load transport of sediment hasnot been well documented except in theColumbia Kiver estuary where, a1 thoughthere is considerable annual variation(Jay and Good 1977), the direction oftransport has been identified by theorientation of bedforms (University ofWasninyton Department of Uceanoyraphy1980). These studies have indicated thatthere is net downstream transport in mostchannels above Tonyue Point, below whichbed load transport reverses direction inresponse to tidal flow. The mixing reyionof the estuary represents d trdnsitionzone for bed load within the channel andhas extremely compl ex bedform patterns.Tagged sediments released at the mouth ofthe estuary duriny the 1980 summer lowflowperiod indicated a yreater (longitudinaldistance) transport out ot the estuaryduriny low tidal ranye than into theestuary duriny high tidal ranye.2.5.2 ChemicalEstuarine sediment chemistry can oecharacterized by the mineralogical andcherni ca I composition of the sediment particlesand associated interstitial detrituswhich, in yeneral, can be related tothe yrain size structure (Burton and Liss1976). Mineralogical composi tion of estuarinechannel sedirnents is quite variabledue to the different physiographic provinces(e.g., Co1 ulnbia Kiver Basin, OreyonCoast Range, Olympic Mountains, CascadeMountains) contributing sediments to PacificNorthwest estuaries. For example,in the Colu~nbia Kiver, quartz, feldsparand volcanic minerals are the dominantconstituents in sand particles; quartz,feldspar and mica comprise the major mineralsin silt; and nrontmori 11 inite, chlorite,and kaolinite are the principal cornponentsof clay (Forster 1972). However,these constituents chanye dramaticallyalong the course of the river, such thatthe contribution of quartz, hornblendeand auyi te decrease downri ver and volcanicrock frayinents and hypersthene becomemore prominent below the Bonneville Dam(Whetten et al . 1969). Thus, hypersthene,cl i nopyroxene cauyi te, and hornblendecharacterize the sediment rnineraloyy ofthe estuary (Venkatarathnam dnd McManus1973; Ni ttrouer 1978), a1 thouyh cl inopyroxeneat the mouth of the estuary isprobably coastal-derived sediment (Universityof Washington Department of Oceanography1980). Cl i nopyroxene a1 so characterizes Grays Harbor sediments (Scheideggerand Phipps 1976). Kulm and 8yrne(1967) recognized three distinctivesuites of heavy minerals in the channelsediments of Yaquina bay--marine, rnarinefluviatile,and fluviatile. Marine sediments,characterized Dy pyroxenes such asdiopside, and nypersthene, extend approximately3 k111 into the estuary; the marinefluviatesuite occurs over approxi~nately6 km and is characterized bd micas, nluscovite, and biotite, with reduced contributionsby metarnorphic minerals such askyanite, staurolite, and si 1 lirnanite; andthe fluviati le suite, characterized bythe micas, hematite, and limonite, occursin the upper reyion of the estuary.Oryanic matter in estuarine channelsediments, principally particulate oryanicmatter (POM), oriyinates from theexcretion by animals and decomposition ofplants and animals and oryanic particlestransported into the estuary which havesettled in association with inorganic(mineral) particles. A variety of measureshave been utii ized to quantify organicmatter. Each evaluates a different

spectrum of the total organic or itsrelative chemical or oiological reactability.These lnclude, but dre not ll~llitedto: I) volatile solids; 2) biochemicaloxyyen denland; 3) chernlcal oxyyen demand;and, 4) total oryan.rc carbon.because settl iny ot oryarlic particles,including those resulttny from flocculat~onprocesses, involves ~as~cdl lytne sdirle processes whlch determine inoryanlcsedlnrentdtlon, tne dlstrlbutlon otoryanic ~i~dtter tllrough an estuary isusudl ly closely i nteyrdted with sedimentsl ze dl strlbutlon. f xceptlons to tni syenerdl ization occur when point sourcesot orydnic matter (e.y., oryanlc pol lutdnts)wltnrn tne estuary dolmnate localscdl~entdtl~n part1 cles. Accord i ng 1 y ,~t~axintua oryanic content of estuarinechdnnel sediments 1s usually correlatedwltti the cllstributiun of tine sedimentpdrtlclcs assocl ated wl th the mlxlny zoneot ttie estudry, wi th vdriation due to( hdnrirl bdthynretry , 11115 correlation i sBrst I 1 lustrated by the dlstrlbutlon otsrdlll~rnt oryarlic ~natter tnrouyh the ~nai n-ste~n channel ot Grays Harbor (Flgs. 2.1dnd L.k$). In yenera 1, pedk concentrationsof setfltlrent organics occur In the innertlarbor dnd central m~xiny zone portion oftltta estudry, particvldrly in associationwittl silt drld cldy tractions (see Fig.2 . Hecause tnu trldnnel slopes andbdnks trave lower (~nte~rated) water veloclt1c2s thin do the chdnnel bottonis, tineorgdnic particles nave a lonyer period ottlti~e clurlng which to scrtle there. As aresult, the channel bank and slope habit.dt5Ot GrdJs HdTDOr t ~ ~ l ~ 11 d1ustrdt-led higher levels of orranics which startedOccurrlny further up the estuary (inland)than did tnose of the cnannel bottonrs.!-or colrtparison, dredge sanlples otrstuarlne channel seairnents In the CnetcoKiver, Coos @ay, Loquil ie Bay, KoyueKiver, Siuslaw say, Umuqua gay, and'r'aqu~nd Bay estuarres nave Rad totalvoidtile sol~ds values ranginy between1 .t33-4.1)4%+ 0.38-8.7 7X, 0.44-0.50%, 1.19-1.34%, O.Zb- 0.61%, 0.91-3.272, and 0.49-tf.78x, resyectivety (Percy et 51. 1974).Estuaries niay act as yeocnemicaltraps for dissolved irraterial throuyh flocculationand sedimentaion processes. Thisresults in a net transter of trace elementsand oryanic matter to sediments(and benthic organi sins), particularly inanoxic habitats where the ptiysi co-chemicalconditions (e. y., redox potential )are conducive to the fixing of trace elementsin estuarine sediments (Burton andLiss 1976). In general, Ni, Co, Cr, V,Ha, Sr, Pb, Ln and Y concentrations aresimilar in 50th drroxic and oxidizing sedirlrentsbut irln, Cu, Se, Zr and Mo, alonywith the major elements of phosphorus,CdrbOn, and sul fur, are colnpatively enrichedin anoxic sedirilents. AM Test, Inc,(1981) reported Cu in sedilrlent elutriatefront (;rays Hdrbor as high as 1.2 my L-1;zinc as nibh as 1.85 "19 L-1; and Pt, ashiyh as 0.12 my L-1. Organic pollutants,incl udi nt, getrol cum hydrocarbons, pesti -cides, PCBs (polychlorinated biphenols),and pu 1 pnri 11contaari ndnt s , a1 so tended tobe more concentrated in the finer sedinrentsadjacent to the channel. Overall,petroleum hydrocarbon concentrations ashigh as ti mg L-1, PCB's as hiyh as 8.4ppb, and pesticides (primarily aldrin andBHC corrtyounds) as high as 4.3 ppb occurredin the elutriates trorlr channel andadjacent sediments in the industrializedreyions of the estuary.Salinities of interstitial water inthe top 6 cln of ttle channel sediment inthe t'raser Kiver estuary were describedby Chapnlan (1981) as having a definiteyradierit structure, garticularly in tnenresohaline region of the estuary, and thatthe rllayni tude of the gradients changedseasonally. Maxi~l~uiri salinity graaationwithin the sedinrent 1 ayers was ooservedto coincide with the spriny freshet. Thissuygests that sedilrlent chemi stry and infaunacoln~irunity structure rnay 5e inf liiencedby this yradient structure overannual time scales, althouyh this has notbeen investigated.

CHANNEL BOTTOM$ 201CHANNEL SLOPEO SOUTH BUOY WHITCOMB CROSSOVER MOON COW POINT COSMOPOLISJETTY 13 FLATS CHANNEL ISLANOFig. 2.7. Volatile solids (% of total dry weight) in sediments atseven channel bottom and slope locations in Grays Harbor.

7 -6 - 8,5 - 1 \4 -I3 - ICHANNEL/O---0SLOPEIBANK\ /1 o---o---od'0 - MID-CHANNEL2 -I , ,_SLOPEiBANKMID-CHANNELz 2-aMIDCHANNELa~ - SLOPEIBANKufK0 0Fig. 2.8. Distribution of organic matter (volatileygen demand, and total organic carbon) in sedimentsbottom and slope/bank 1 ocations in Grays Harbor.solids, chemical oxatfourteen channel24

2.6 ITEMILATIUN AND CLASSIFICATION dF cl assi fied dccordi ny to their dorni nantESTlJARINE CHANNEL HABITATS IN channel nabi tat characteri stics. Tab1 eREGION 2.1 lists the estuaries, their extent,type, morptIology , slope, and substrateA total of 116 estuaries in the Pa- characteristics for those where suchcific Northwest have been identi tied and information is known.

Table 2.1. Locations, characteristics, and classification of principal estuarine channel habitats in the Pacificfiorthwest. See text at end of table for further explanation of classification categories. Data sourcesincluded USGS (1978, '1980); Uilliams et al. (1975); Smith et al. (1977); U.S. Army Corps of Engineers (1976);Proctor et al. (1980)); and Johnson and Gonor (1982); British Columbia data for 1981 only (Environment Canada1982) .Totalkverage Annuat €GentDrainage Annual Mxinu EstuarineArea Ui srhar Area Estuary Channel Bar@Estuary Wdterfheds (kd)Type1 lbrpholo& slope3 substrate4(Cal rfornia)Eel River Eel River 8,9M 7,322 21,776Salt River - -Humboldt 8ay Elk River -Jaco~eCreek - -62Salmn Creek - -Fresnwater Creek - - -Mad Kiver Ebd River 1,256 1,336 2.290ORLittle River1'2 Kedwood Creek01Klamath RiverSmith HiverLittle KiverRedwood CreekKlamath RiverSmith Hiver(Oregon)Winchuck Hi verChetco BayPistol RiverRoyue RiverElk RiverSixes KiverCojuil le BayCoos BayUmpqua Hi verSiuslaw RiverWi nchuck Hi verChetco KiverPistol RiverRogue RiverElk RiverSixes RiverCoquille RiverCoos Riverlstnmus SlouyhSouth SlouyhUmpqua RiverSiuslaw River

.r .-P: rL LLmL L Y ma, LaJY Y LU a, Y L5 5 a,L >L L w w m u > L L > W a ,m L.-.r >La, LL.?a .rL w aJ . r w > - Y a, ~ a , $ F,:: L w w w a> La, > W L.- a,w .- >u > u a m Y > w .- .-r >L Y .- .r a, Y.7 >Y xZ.~>U U ~ E E > E ~ > > L wXL x c m z w 0 CL .-v, Z" m a, .r U L 0 r v , ,:$ .-Y X m , r w Z Z P I X 4 C L K >CL-CE-4-1 c c N C 3 UO, u E c .-n v, m- m n .r - m m a- m E U m 3~ch.r L W C , @ ' - ~ - + I ~ csc =aU m ~ D -5 - m m ~ , c --m- c 2% - c 3 m 3 m m 3 L - m - L O x s w m w Em U m .rU m a, W.- a .-.-.-.- 01 m a 000 L a, ~ m 0 0 mSc.r 0 a, 0s.r 0 3m m m .- CJO mo.-c - c m ~ m m m v , -SSX.-~GL P:~~Y.-+I=- 4 W > WW wl Z Z L WJ I-XLY L ZZ U3S3-2 P Z m Z a Z 3 Z U W 3 U 3 1 1Lh.F w o n m P: - m'Y h 9 .r .r a , m ~ 10m Y x m Y" 5 m Em n m .,-u m m o E U C , m+.' C N c z u 2 - w . r 0 J, Q* m . r e 0 0 3 L 5 - C mw E x + o m m 5.5 U v , 0-7 - # A * c u - S U 8 -YLa, h '?! kwL L a , ? 'r >> 4 z w L m h 10 h Y 'Cm - m . - a Y o .-< zwl m 2 2 ; Z z z u m 223-

Quinaul t River Qujnaul t River 1,124 2.520 l,4M BB FBB H? M G-S08 F? M GOueets R3ver Queets R~ver 1,153 3.690 3,bW Bl3 F M GKalalocn Creek Kalalocn Creek BB n n ti- SHoh Rtver Hoh River 774 2,240 1.3W BB F M I;-S(ioodtnan Creek Goodman Creek 82Vui llayute R~ver mi 1 layute River 1,629 F M G- SOzette River Ozette Hiver 229 45 BI F M tiMukkaw Bay Waatch River 33 35-a3 Sooes River 105 95Sai 1 Rf ver Sai 1 River 14 - 20HGSekiu RiverHoko KiverClallam BayPysht KiverLyre RiverFresnwater BayNew Uunyeness layUi scovery BayPort Townsend SaySekiu RiverHoko RiverClallam RiverPysht RiverLyre RiverEfwna RiverUunqeness HiverSnow CreekDean CreekCnimacum CreekPort Ludlow Ludlow Creek - FSquami sh Harbor Snine Creek - - FThorndyke Bdy Tnorndyke Creek 31 F

Taraoo Bay Tarboo Creek 32Jackson CoveMarple CreekSpencer CreekQui 1 cene Bay 0i y Qui 1 cene RiverLittle yuilcene Riv.Dosewall ips River Dosewall ips Hi ver -Duckabush River Duckabush River 172G-Sti-sG-SHamma Harnma Ki ver Harnma Ki ver 219Li 11 iwaup Bay Lilliwaup Creek -Annas Bay Skokonlish River 622Big Mission CreekRig Mission CreekLynch Cove Union Hiver 6 1Tahuya RiverTahuya RiverOewatto Bay Dewattor Ki ver 48Anderson Cove Anderson Creek -Stavis BayStavis Creekti-Sti-sti- sSeabeck BaySeabeck CreekLittle Beef Harbor Little Beef CreekBig Beef Harbor Big Beef Creek 36Port GambleAppl etree CoveMiller BayGamble CreekMiller LakeAppl etree CreekGrovers CreekLiberty BayDogfish CreekDyes InletClear CreekStrawberry Creek -Chico CreekSinclair Inlet- Gorst Creek -(continued)

Table 2.1.Concluded.TotalAveraye Annual ExtentDrainage Annual Maximum EstuarineWatershedsArea Dischar e Dischar e Area Estuary Channel Bank(km2) m 3 y ) (m3 e (kin2) Typel ~orpho1oy.y~ Sl ope3 substrate4Olalla BayGig HarborBurley LagoonCase InletHammersley InletOakland BaySkookum InletOyster BayEld InletCapitol LakeHenderson In1 etNi squal ly ReachChambers BayComnencement BayShilshole Baytverett HarborPort SusanSkagit BaySamish BayBe1 linyhd~l~ bayDrayton HarborOlalla CreekCrescent CreekBurl ey CreekRockey CreekCoul ter CreekSherwood CreekMil 1 CreekGo1 dsborough CreekSkookum CreekKennedy CreekDeschutes KiverWoodard CreekNi squal ly RiverMcAllister CreekChambers CreekPuyallup HiverCedar KiverLake WasningtonSammamish LakeSnohomi sh Hi verStillayuamish HiverSkayit KiverSamish KiverNooksack KiverDakota CreekCalifornia Creek

LwL > w L CwL2 0 1 Cw :'a .- C P C . r . Y > Y . -c 2 a m a e m m w . w E - ' ]o o r m m L O *V) E . . - r u u c '2 .- v,.r m U .- w m La m - ' 2 4 , . ,3 c0 m rs L U UW n C,z s s z gI

CHAPTEK 3PR IMAHY PRODUCTION IN ESTUARINE CHANNELSThe production of plant biomass and Stockner (1976) listed five speciesthrough the photosynthetic. fixation of Ot diatoms - Melosira 111onil ifor~nis, M.mCarbon occurs at several phyloyenetic cf . n ~lnm~l~ides, Navicula cancel lata, - N.levels in estuarine channel habitats. grevi I lei, and Pleurosi nia zestuarii - asThis primary production is yenerated by dominant in the ----?centra det ta region ofboth algae and true flowering plants or the Squarnish Kiver estuary; N. ~revilleianyiosyern~s. Estuarine a1 gae, however, was the one species noted to occur partiarea taxonomical ly and ~norpholoyically cularly in 1 ittoral flat (tidal) channeldiverse yroup of flora, includiny epiphy- habitats from January to May.tic single-cel led nli~rophytobenthos andpelayic phytoplankton (i l , diatoms, 3.2 MACKOAL(;AEdinoflagel lates), epi benthic filamentousforms, and sessile ~~racroalgae (i.e., sea- As with tne rnicrophytobenthos, sesweeds,kelps). Estuarine anyiosperms are si le macroalyae does not characteristicusuallylimited to seayrasses, principal- ally occur in estuarine channels due toly Zostera spp., but can also include 0th- the usual water depths and unstable, fineersubmerged dquatic plants such as pond- textured substrates. Similarly, the not-Zannichell ia able exceptions would include shal low- lum spp., and --- Elodea spp,Cerabophyl- channels with low current velocities,i .e., blind dendritic channels on 1 ittora1flats, and channel banks with natural3.1 UENTHIC MICKOFCUKA or artificial cobble to sol id rock substrate.Macroalyae are also found at-Estuarine microflora (microscopic tached to artificial substrates such asplants) typically includes benthic microalyac such as diatoms (Uaci 1 lariophyceae)pi 1 inys, buoys and bulkheads.which occur on or in the upper 1 cm of A1 though not as diverse and robustbottom sediinents, a1 thouyh I iving diatoms an assemblage as the marine seaweeds andcan be found as deep as 18 cm as a result kelps, there are a number of estuarineof die1 vertical nliyration within the macroalyae which are widely distributedsediment (McLusky 1981 ).and highly productive within the narrowsalinity and substrate conditions theyA1 though microphytobenthos often con- are adapted to. These generally includetribute the major portion of the primary+various blue-green algae and species ofproduction in littoral flat habitats of Enteromor ha spp, and Fucus sp.; in thePacific Northwest estuaries, the unstable Pact rc Northwest the specific taxa arebenthic environs of estuarine channel hab- E. clathrata var, crinita, E. intestinalitatswould suyyest that; lnlcroflora assm- -is, E. 1 inea and E. distichus. O t h e r sblayes are relatively 1 imi ted in these d~miiiantr~haline mat- gae includehabitats. Notable exceptions might be in Monostroma arcticum, E.the case sf shallow bl ind or subsidiary ma, Ulvaf lexuosa, E. minichannelswherein bottom sediments are morestable; unforunately, practically no infannationexists relative to species corn-position or Structure of microflora in es- eroy and Stockner (-indicated that L.tuarint channels of thi s region. Pomeroy riparium and V. dichotoma are macroalgae-32

epresentative of 1 ittoral channel habi- in estuaries, nannopl anktonic diatoms aptatsin the Squamisn Kiver estuary.pear to be the ~rlost abundant forms durinythe summer and fall periods of peak phyto-3.3 ANGIOSPERMSplankton production (Stockner and CliffThe principal taxon of angiosperms or1979).true flowering plants common to PacificProctor et al. (1980) identified 34Northwest estuaries is eel yrass, Lostera taxa of diatoms as characteristic of estuspp;this includes the principal indigen- arine channel habitats; ot these, Chaetooussuecies. -- Z. marina. as we1 1 as a rarer ceros spp., Melosi ra spy., and Skeletonemaspecies, Z. noltii (= Z. arnericana). costatum were considered abundant, andWhile L. natii-rs in only in littoral Achnathes spp. and Lauderia spp. werezones l~itchock and Cronuuist 1973). Z. considered common constituents. Karentzmarina ' occurs in sub1 itt'oral zones ad, and McIntire (1977) listed the 42 ntostas with the benthic alyae, may be found abundant diatorn taxa in Yaquina Bay, ofin shall ow, non-mai nstem channels. Sub- which Cvlindroutvrxis so.. Chaetocerosstrate structure, in addition to tidal subti 1 is; ~elos'ir"a sulcat'a,. Thalassiosiraelevation and current or wave action, ap- decipiens, - C. socialis, - C. debilis, Amphipearsto be a principal determinant of prora paludosa, and Surinel la ovata corneelyrass distribution and abundance. Al- pri sed more than five percent of the totalthouyh eelyrass can be found growing in cell count. Anderson (1972) described disubstratesranyiny trom soft mud to grav- atoms of the inshore reyion of the Columelmixed with coarse sand, its optimum bia Kiver plume as originating in partsubstrate composition appears to be muddy from the estuary. This assemblaye wasor silty sand with median yrain diameters dominated by Asterionel la formosa, Meloof-250 pm (2 4 ) and sortiny below 500 pm sira islandica, and Thalassionerna nitz-(1.0 4) (Phillips 1974). Eelgrass beds schioides durinu the winter and bv a richin Grays Harbor persist in habitats where flora of predo~n~nantl~ Asterionel la japonfinesand (62-500 m) predominates (J.L. - ica, Chaetoceros comyressus, C. radicans,Smi th et a1 . 1976) . Eel grass occurrence Rhizosolenia alata, R. alata-graci 11 ima,in Coos Bay was related to the organic - K. delicatul'a, and: frmssima durinycontent and turnover rate of sediments the summer. The diatom assemblaye in the(Oregon State University 1977). A Columbia Kiver estuary in April and Maydetailed synthesis of information on eel- 1980 was found to be dominated by a relasrass"ecosvstem" anpears in Proctor et tively few freshwater species, includinyal. (1980; Skction 3.211.3, Vol. 2).primari ly Asterionel la formosa, Melosirai slandica, M. distans, Stephanodiscus3.4 PHYTOPLANKTONhantzschii, iid S. astraca var. minutulaIOreuon State ~nfiersity School oi' Ocean-Although perhaps not developed tothe extent that phytoplankton populations?n rnore stable, less turbid marine (e.g.,oceanic) or estuarine (e.g., fjord) habitatsare, phytoplankton of estuarine channelsundoubtedly constitute the principalsource ot autotrophi c production in thesehabitats. Three functional size groupscan be said to typi ty phytoplankton: 1)ultraplankton, (2 pm, consisting of principally bacteria; 2) nannopl ankton, 2-20unl, consisting of sinall diatoms and microf1 ayel lates; and 3) microplankton, 20-2UUput, consisting of larye diatoms and dinof1 aye1 1 ates. A1 thouyh dinof lagel latesare occasional ly abundant (McMurray 1977)ograihy 1980b). The of uniquelymarine, estuarine, or riverine phytoplanktonor a combination of these assemblageswithin one channel location in an estuarywi ll depend upon circulation transport andnlixiny of water masses, which are highlyvariable over short-term (tidal) andlong-term (seasonal) time scales (seeSection 2.3).Dominant phytoplankton taxa durinyspring blooms in Burrard Inlet (SeymourRiver estuary with some influence fromFraser Ri ver) i ncl uded Skel etonema costa-- tum, Certaul ina beryonii , and Thalassiosiraspp. in the outer inlet; - S, costaturn-7

ana Coscinodiscus spp. in the inner inlet;and S. costatum and Thalassiosira spp. in~ndiiin and Port Moody Arms (Stockner andC l i f f 1979). Dominants during fall bloomswere somewhat different: C. beryonii inthe outer inlet; S. costatiim, Thalassio-thrix sp,. and c.-beryonii in the inner-inlet; and C. costatum, nitzshcia spp.and Exuviell? sp. in Indian and PortMoody Arms.3.5 ESTIMATES OF STANDING CROP ANDPR IMAKY PRODUCTION RATESTwo aspects are generally consideredin evaluating autotroyhic production: 1)the distribution of the producer biomass(standing crop) and, 2) the rate of photosynthesis.Measurements of physical andchemical parameters influencing these twoOariables are a1 so documented simul taneouslyin order to determine the environmentalfactors control l iny the fixationof plant carbon. Microflora and phytoplankton standing stock are typical 1yassessed by: 1) chlorophyll a concentrationi., y cm-3 or my-m-3); 2)particulate carbon and nitro en (C/N); or3) gravimetric i.. , my L-7 or my m-3)analyses, Macroalyae and anyiospermstanding stock is commonly ex ressed inyravimetric terms (i.e., y m- B ). Ratesof primary production of microflora andphytoplankton are yenerally estimatedthrough either 1) measurin labeled carbonuptake ( e . mg C - hr-1) duringincubation at representative 1 ight 1 eve1 sor, 2) measuring oxygen evolution or uptakeover an incubation period, whichyields both production (i.e., mg C m-3hr-1, mg C nl-2 hr-1) and respiration rateinformation.A1 though estimates of mean primaryproduction of micro hytobenthos as hi yhas 108 mg C IR-2 hr- Y have been documentedfor a 1 ittoral flat habitat in the ColumbiaHiver estuary (Mclntire and Amspoker1981), most gross l~rimary production rateestimates in lower 1 ittoral habitats ofthat estuary and in Grays Harbor (Thom,unpublished) average 0.5 my C m-2 hr-1.Given the increased water depths, lowertemperatures and unstable benthic conditionsof estuarine channel substrates, itis likely that production rates in thesenabi tats are significantly lower and morevariable than are those of littoral flats.Pomeroy and Stockner (1976) described productionof channel -type diatom asse~nbl ayeson the Squamish River estuary as ranyinbetween approximately 0.5 and 1.0 g C m- !day-1, although tnese were not obtainedfrom cnannel habitats per se.--Gross primary production of estuarinemacroal gae on I ittoral flats in GraysHarbor was found to ran e between approximately1.5-2.5 g C m-2 hr-1 for Enteromorphaclathrata var. cri ni ta (A-,1.0-1.5 g h r - 1for E.intestinalis(Auyust), 0-0.3 y C m-2 hr'=l for E. linza(June) and 0.5-1.0 y C m-2 hr-l for Fucusdi stichus (June, August) (Thom, unpub-Pomeroy and Stockner (1976) indicatedthat strongly euryhal ine macroalgaeassemblages were generally less productive(mean production of 0.6 g C m-2day-1) than weakly euryhal ine assemblages(2.2 y C m-2 day-1) on the Squamish Kiverestuary delta. These production valuesare pr0baDly also representative of estuarinechannel macroalgae which are distributedin high sublittoral elevations.Production of epiphytic macroal gae on Zos-- tera blades has not been estimated butepiphytes on Thalassia have been estirnatedto equal 20% of the estimated averagenet production of that seagrass inFlorida (Jones 1968).Rates of primary production by eelgrassvary considerably over the temperatedistribution (circumpolar) of Losteramarina, in part a function of the widerange in turion densities within eelyrassbeds (Proctor et al. 1980) and in standingstock, which varies between 6 and 5157 g(dry) m-2 (McKoy and McMillan 1977).Production estimates within the PacificNorthwest region exist only for PuyetSound and range between 0.16 and 1.9 y Cm-2 hr-1 (Phi 11 ips 1969, 1972).Phytoplankton biomass and productionhas been systematically measured in estuarinechannel habitats of only YaquinaBay (McMurray 1977; Johnson 1981), theColumbia River (Haertel et al. 1969;Oregon State Uni v. School of Oceanography

138Ub), and the Eraser Kiver estuaries(Takatlastli et a]. 1973; Stockner and Cliff1979). McMurrdy (1977) found standinystock duriny the spring phytoplanktonblooril in Yaquina Bay to range betweer171.1 and 1.1 x 108 y ~ n and - ~ productionto range between 4.7 and 172 my C m-3nr-1 over the same period. Johnson's(1981) studies of upper Yaquina Bay betweenJuly and November 1973 and 1974 documentedan average phytop I ankton standinystock of 5-6 my m-3, while ri~aximum productionof 78 to 104 ing c ma3 hr-1 occurredin July and Auyust. Chlorophyll a measureinentsof phytoplankton biomass-i n theCol urrlbia River estuary between April andNovember 1980 varied between approximately1 and 18 my m-3, with the hiyhest valuesoccurriny froin May throuyh July (OreyonState Univ., School of 0cea.nography1 J80b). Higher biomass concentrationstended to occur in the upper, riverineregion of the estuary and lower values inthe downstream, marine region. Spatialvariation indicated rriore hornoyeneityabove the estuary's lr~ixiny zone regionand extreme variation in or near subsidiarychannels (i.e., Younys and Lewis andClark Rivers). Primary production measuredas carbon uptake peaked at between25 and 35 mg U in-3 hr-1 duriny July.A1 thouyh sirni 1 arly high production wouldhave also beer7 expected in May because ofthe hiyh chlorophyll a values at thattime, the eruption of Rt. St. Helens andthe resulting increased inorganic suspendedsediment raised the level of liyht extinctionof pnytosynthesis (see Section3.6). Phytoplankton cells less than 101!1i1, which predominate near the mouth ofthe estuary, and greater than 33 prrl,which predominate in the upper estuary,accounted for most of the production.Stockner and Cliff (1979) indicatedthat chl orophyl 1 a yeneral ly decreasedfrom a maximum of-approximately 800 mym-2 in the poorly flushed, upper reach(Port Moody Arm) of the estuary to lessthan 150 my in-2 in the more seawardstations in outer Burrard Inlet. Thefjord-type estuarine habitats of innerBurrard Inlet and Indian and Port MoodyArms showed peak primary product ion ratesof between 4 and 6.6 y C m-2 day-1 durinyspring and autumn bloOinS, 1-2 y C lr2day-1 in the sulllmertially neyliribleinterim, and essenproductionDetweenNovember and Mdrch (Stockner and Cliff1979).A number of abiotic and biotic fdctorscontrol or inf 1 uence the [~roduction,distribution, and abundance of autotrophically-produced carDon, and the fate oftne different siicro- and macrophytic producers.1 hese re1 at i onships are conceptuallyillustrated in Fiy. 3.1. A11 producersutilize l iyht and nutrients as thebasic ingredients in assembliny oryanicn~olecules, initial ly carbohydrates (glucose)which are transferred and transformedinto amino acids, protein, andother complex nlo1 ecul es essential fororydni sins' survival , growth, and reproduction.As the universal element involvedin these biological reactions, carbonis yeneral ly regarded as the most appropriatecociunodity to map energy flowthrouyh the ecosystem.In addition to tne photosyntheticinyredients of 1 iyht and nutrients, otherphysical parameters such as temperatureand salinity control the yross rate ofbi oloyical reactions. Uther envi ronmentalvariables such as vertical mixinythrough the water co'lumn, liyht attenuation,substrate structure and stabi 1 ity,and shading regulate the magnitude andextent ot solar radiation available toproducers and thus ul tirnately affect bothbiomass and the rate of production bythese oryanisms. Toyether, these variablesare considered driving variables(inyredients or conditions 1 imi ting photosynthesis)and control liny factors (affectingthe distribution of producers,prirnari ly through physical or rnetaboi iceffects).RIntire and hspoker (1981) indicatedthat structural properties (meanyrain size, skewness, sortiny coefticient)of mudflat Sediments in the Columbia Kiver estuary were highly correlated

Fig. 3.1. Primary production compartments and driving variables and 1 imiting factorsinfluencing distribution, standing crop, and rate of production in estuarine channelhabitats of the Pacific Northwest.with the biological variables of microafgalbiomass and production. The lack ofany significant correlations with 1 iyhtintensity and temperature suggests thatthe microphytobenthos is hiyhly adaptedto achieve their maximum photosyntheticrate at relatively low light intensitiesand temperatures. Thus, substrate characteristicsmay be the more critical factorinfluenciny standing crop and grossproduction, by regulating the ability ofmicroalgae to colonize and persist inhabitat. Welch et al. (1972) found thechlorophyll 5 concentrations of periphytonon submerged artifici a1 substrates inthe Duwami sh Ri ver estuary di rectly corre-1 ated with light intensity, includingthat caused by increased water turbidityresulting from a rainy period. Temperaturewas relatively not as important afactor. The spatial distribution ofperiphyton, however, in the UuwamishRiver estuary appeared to be regulated bysalinity structure.Phytoplankton biomass distributionand production are even more affected byhydro1 oyical conditions within estuarinechannel habitats due to the influences of

vertical mixing of the water column. ~ 1 -though inorganic nutrients, particularlynitrogen, were found to be potentiallylimiting in late spring and Summer in theColumbia River estuary, 1 ight attenuationin the water column was Considerd to beof primary importance in controlliny theamount of photosynthesis per unit phytoplanktonbiomass throuyhout the year(Oregon State University School of Ocean-ography 1980b) - A simulation model ofphytoplankton photos~nthesis and growth inthe outer reaches of the Fraser River estuaryindicated that nitrate levels were1 imiting duri ng the summer, that temperaturewas limiting production near the surfaceduring the winter and spring, andthat light was the Principal limiting factorat the surface the rest of the year,and at depth throughout the year.

UETKITUS PKUCESSING IN ES'TUAKINE CHANNELSIn addition to the various primaryproducers characterizing estuarine channelhabitats, described in Chdpter 3, the roleof oryanic detritus as potential sourcesof trophic carbon transported into andmade avai 1 able within the channel habitatmust be considered. Recent evidence tlasi 1 lustrated that, directly throuyh detritivoryor indirectly through heterocrophicprocesses, detritus may constitute thedominant pathway of trophic carbon intoestuarine food webs (Darnel1 1961; Odum1970; Qasim and Sankaranarayanan 1972;Shubnikov 1977; Correll 1978). Detritusmay also have a valuable role in stabilizinyestuarine systems by leveling outtne seasonal variations in primary production(McLusky 1981).Darnel l (1967) has aefined oryanicdetritus as "all types of bioyenic materialin various stages of microbial decornposition which represent potential eneryysources tor consumer species." Uetritusincludes both particulate and "subparticulate"matter. 8y the reference tomicrobial decomposition and utilizationby consumers, this definition appears tobe 1 i~nited to what is commonly referredto as fine particulate oryanic carbon(FPOC). Since much of this material hasoriyinated trom much laryer organic particleswhich were inechanically or biochemicallyreduced to FPUC, this definitionshould be expanded to include any free(non-attached) particles of organic matterwhich no longer, if ever, produce carbonthrouyn photosynthesis. Included in thisexpanded definition, therefore, are biogenicparticles of both plant and animalorigin as we1 1 as free-formed (throughchemical or geological processes) partic1es, and includiny associated sorbed dissolvedsubstances an5 the residing microbes(Christian and Wetzel 1978).4.1 DETRITUS SOURCESUnfortunately, there is scant i nformationto indicate the sources of detritusthat are produced within or transportedinto estuarine channel habitats of theregion. Thus, only speculative inferencescan be made of the relative contributionof potential detritus sources.Detritus which is usable by estuarine channel detritivores, considered tobe primarily FPOC, is derived from threeorigins: 1) that entering the estuary alreadyin FPUC form, previously colonizedor immediately colonized by microbes oncein the estuary; 2) that enteriny the estuaryas laryer particles (LPOC) and,through mechanical and microbial action,beiny reduced to FPOC within the estuary;and 3) that formed by the creation of organicparticles (Darnell's [I9671 subparticulatedetritus) throuyh the process offlocculation of dissolved oryanic carbonwhich has been either transported into orgenerated within the estuary (Fig. 4.1).Both particulate and dissolved carbon canenter via riverine or marine inflows orcan be derived froin autochthonous productionwithin the channel or in associatedestuarine habitats.Organic particles deposited into riverscan include tree leaves and needlesfroin forested watersheds as well as treebrancnes and whole tree trunks. Detritalparticles indigenous to the river includephytopl ankton, other (periphyton) a1 yalcell s , zooplankton exuvi ae and feces, andfish and other freshwater animal feces.Marine detritus includes detached macroalgae,phytoplankton cell s, zooplankton exuviaeand feces, and fish and other animalfeces. In addition to similar macrophyteand animal sources, detritus particles

RlVERlNE SOURCESMARINE SOURCESFig. 4.1. Potential sources and pathways contributing to detritus in estuarine channelhabitats of the Pacific Northwest.produced uniquely within the estuaryinclude abscised eel grass blades and rhi -zomes and estuarine marsh plants. Inaddition to the influx of sinking phytoplanktoncells, mats of benthic microfloraestablished on littora flats arefloated off the flats and into channelhabitats during hiyh tide cycles (C. O.McIntire and M. C. Anispoker, Oreyon StateUniv., unpubl. information).Dissolved oryanic carbon (DOC) in riversis considered to be primari ly al lochthonous,derived from the leachiny of terrestrial1 itter, 1 iving vegetation, andsoils (Fisher and Likens 1973; McDowelland Fisher 1976; Mu1 hol land 1981) ; however,the contribution of autochthonousfreshwater sources such as leachates fromaquatic macrophytes and phytoplankton andexcreta from aquatic animals has not Deenfully evaluated. Marine DUC, on theother hand, is essentially autochthonous,ori yinating from leaching by zooplanktonand from animal excreta; some leachatesfrom nearshore marine a1 yae and a1 yal detritusmay also constitute an unknown portionof marine DOC. The generation of DUCwithin the estuary, however, may surpassthat of both riverine and marine sourcesdue to accelerated leaching of extracellularDOC from the extensive 1 ittoral algaeand saltmarsh rnacropnyte assemblayescommon to Pacific Northwest estuaries.Leaching or excretion of DOC has alsoheen tound to be appreciable in phytoplanktonand periphyton (Anitd et al.1963; Hellebust 1965, 1374; Fogg 1366,1977) and in marine and estuarine macrophytes(Cragie and McLachlan 1964;Sieburtn and Jensen 1969; Sieburth 1969;Vel imi rov 1980). Mann (1972) suyyestedthat over 90% of the production of marinemacroyhytes enters the coastal marinefood web as dissolved organic matter.

Sieburth (1969) calculated that 30% ofthe totdl carbon or 401 ot the net carbonfixed daily by the littoral fucoid, Fucusvesiculosus, is exuded as DOC. Muc3i-Xthis exuded DOC is apparently comprisedof dissolved carbohydrates, which Burneyand Sieburth (1977) estimated to accountfor 10 to 20% of the total DOC in NarrayansettBay, Rhode Is1 and.Formation of FPOC from UUC throughthe formation of molecule masses calledaggregates has been postulated as a majorsource of detritus in estuaries. Increasedparticle sedimentation resultsfrorn formation of larger, denser agyregates.Ayyreyates from suspensions ofclay and phytopl ankton particles form inthe presence of electrolytes such as wouldbe encountered in estuarine mixing zones(Anvimelech et al. 1982). Although theexact mecnani s~n of aggregate formationfrom DOC is not well defined, the actionof bubbles risiny to the water surfaceand bubble forrndtion at the air-sea interfacewhere oryanics tend to De highly concentrated(Harvey 1966; Goering and Wallen1967 ; W i l l ia~ns 1967 ; Ni shi zawa 1971) appearto be important processes in creatingthe surface required for d particle nucleus(Ka~nsey 1962; ilaylor and Sutcl iffe1963; Ki ley 1963, 1970; Sutclitte et al.1963; Kiley et al. 1964, 1965; Krone1978; Wallace dnd Duce 1978). i3arber(1966) concl Uded that microoryani sms wererequired in aygregate tormation but thecurrent evidence suyyests that bacteria,oryanic, or inorganic particles can allact as the nuclei for initiatingayyreyation,Tne formation of detrital ayyregatesis accelerated in estuarine channel nabitatsas a result of several physical andctlemical processes that occur with themixing of saline and fresh water. Theseprocesses in consort account for "saltf 1 occul ati on," wherein even extremely 1 owsalinities promote the precipitation,f 1 occu t ation, and agyreyat ion of di ssol vedoryanics into organic detritus particlesprone to higher settling rates (Siebruthand Jensen 1968; Gardner and Menzel 1974;Sholkowi tz 1976). While it is apparentthat both chemical (i.e., ionic attrac-tion) and physical (i.e., increased particle~0lli~i0nS alony salinity yradients)mechani srns are interrel ated in fl occul a-tion (Krone 1978), no definitive work hasbeen performed to isolate and define thefunctional processes of FPOC for~nationf ro~n DOC.Avnimel ech et a1 .Is (1982) experimentson the flocculation and sedimentationof algae-clay ayyregates in thepresence of an electrolyte suyyested thatincreased clay concentration would prornoteincreased flocculation and sedirnentai tonof a1 yae if the availabi 1 ity of aygreyatenuclei is a 1 imiting factor. This impliesthat flocculation of a1 yal detritus inPacific Northwest estuaries would be enhancedgreatly duriny spriny freshets whensuspended sediment 1 oads entering theestuaries are at a rnaxin~urn.Therefore, sources of oryanic detri -tus to estuarine channels, whether dissolvedor particulate, depend upon associatedterrestrial, marine, and estuarinehabitats, and within the channel are theproduct of d number of complex and interrelatedestuarine circulation and chelnicalprocesses which have not yet been successfullysorted out. Nairnan and Sibert( 1978) presented a seasonal ly-st ructuredernpi rical budget of organic carbon andnutrient inputs trom the Nanaimo Kiver tothe estuary and concl uded that, comparedto in situ primary production in the rnudflatlhabitats,fluvial DOC (estimated tobe 2 x lo3 g C m-2 yr-l) imported into theestuary via the river may be the yreatestsource of carbon to that system. Hiverineinput of allochthonous FPOC was estimatedto equal 56 y C m-2 yr-1 and to be atleast half derived from the river's periphytoncommunity. Uahm et al. (1981) estimatedthat in 1974 the Columbia Riverexported approximately 5YU.4 x 1U3 metrictons of total organic carbon (TOC) ofwhich 891 was DUC and 11% was POC; overhalf of the annual TUC entered the estuarybetween April and July, 16% of it in June.While the TOC and DOC levels were mosthiyhly correlated with river di scharye,POC was correlated with primary productivity upriver.

In addition to C:N ratios (Mann1972), liynin degradation products(Gardner and Plenzel 1974; Hedyes and Mann1979; MacCubbin and Hodson 1980), andvarious chelnical isotope characteristicsused to t ingerprint sources of detritalmatter (Peters et al. 1978; Sweeney andKaplan 1980; Estep and Dabrowski 1980),the ratio of two stable carbon isotopes,c13/~12 (abbreviated as 613~), has recentlybeen utilized to identify the yossibleorigins of oryanic carbon present in consumeroryanisrns. This is possible oecausethe 1 3 values ~ of an animal 's tissues areusually unaltered trom those of the Carbonin its food source (DeNiro and Epstein1978; Teeri and Schoel let- 1979). This approachhas been used, apparently successfully , in documenting the importance ofvdrious carbon sources to estuarine andmarine detritivores (Thayer et al. 1978;Hai nes dnd Montayue 1979; McConnauyheyand McKoy 1979; Frj 1981). Using liyninoxidation products in conjunction wi th613~, Hedges and Mann (1979) indicatedthat the POC from the Columbia River depositedin offshore sediments was dominatedby yymnosperm woods and non-woodyangiosperm tissues.Usiny 14c-label ling techniques,Sibert et al. (1977b) amassed evidencethat the production of detri t ivorous harpacticoidcopepods in the Nanaimo Riverestuary (see Section 5.3) was supportedpredomi naniy by the bacteri a1 f 1 ora associatedwith oryanic detritus which waspresumed to originate from several exogenousand endogenous sources, including:(1) meadows form the seaward areas (2)alyae from intertidal areas; (3) sdltinarshplants from landward areas; and (4) downstreamtransport from the upland areas ofthe estuary's watershed. In their v?cent613c studies of detritus-based food websin Hood Canal, Wissmar and Si~nenstad(Fish. Kes. Inst., univ. Wash., unpubl.data) have found the detritus Sources tovary seasonal 11, with shi ftiny contributionsof riverine, marine and endemicestuarine-produced carbon. At the Sametime, a considerable recycling of autoch-thonous carbon within the estuary was aprominent characteristic of the detritivorecomponent of the estuarine foodweb.41Very little inforrrlation exists onthe deposition, distribution and flux ofdetritus in estuarine channels, and ~irtuallynone exists for the Pacific Northwest.Pickral and Odum (1976) found thatthe non-uniform distribution of detritusin a Viryinia saltrnarsh tidal creek relatedto the morpholoyy and hydrdul ic regimeof the creek. They deduced that detritusparticles, hydrodynalllical ly equivalent totine sand and silt particles, tended toaccumulate in low velocity zones insidemeanders and behind si 11 s ; storlri events,however, were responsible for periodical -ly flushing detritus accumulations frornthe tidal creek.The flux ot detrital particles withinchannels probably occurs in conjunctionwith the sediment bedload and 1s lnfluencedoy similar tactors (hection 2.5.1).Accordinyly, variations in boundary layervelocities determine the size distribution,flux, and accumulatior~ of detritusparticles through channels, Uepositiondlreyions, where current vel ocities arelowest, would be expected regions ofdetritus accumul ation. Thi s is observedin blind or subsidiary channels with lowervel oci ty reyiines which tend to accumuldtemore detritus tnan do mainsten1channels.But, as with suspended inoryanicparticles, the inainstern channels in !nixinyor entrapment zones of estudries alsoprobably constitute locations of maximumsettl ing of organic partic 1 es and inoryanic-oryanicparticle agyregates. A1 thoughthe lony-term net transport is probablyseawdrd, detritus particles may rernai nwithin this zone for periods lony enouynto be extensively uti 1 i zed by detritivores.Naiman and Sibert (1978) pointedout the importance of "retention structures"as traps of oryanic detritus, andidentified oyster beds, macroalyae, andspaces around coobles as FPOC retentionstructures and logs and eelyrass as LPOCretention structures. To this list snoul aalso be added the eineryent plant assemblayesof estuarine salt marshes. Theyconc I uded that fjord and drowned river

valley estuaries, with 1 ittle oceanic ly 10-11% as only iparticulate carbon wasexchange, l arye areas, and nunlerous types utilized.of retention structures may be the mostefficient retainers of a1 ~ O C ~ ~ ~ O ~ O U S We generally know very 1 ittle aboutdetritus.the microbi a1 assemblages characteri zi nyPacific Northwest estuarine channels, al-4.3 FUNGI AND UACTEKIA COLUNIZATIONthough Wiebe and Liston (1972) includedestuarine channel sampl es in thei r analysesof aerobic, nonexactiny , heterotrophicbenthic bacteria of the Wasninbton andOreyon qoasts. The highest individualcounts (x = 55,925.9 + 23.7 viable counts~icrooryanisms, primari ly bacteria,fun5i, and protozoa, rapidly co1 onizefresh detritus particles and are laryelyresponsible for conditioning detritus tothe stage where it is pnysically and nutritionally viable for consumption bydetriti vores and other primary consumers(Fenchel and Jdrgensen 1977). Harrisonand Harrison (1380) indicated that inmi crocosrn experiments, fresh Losteramarina blades supported a two-week bloomdfspended bacteria. They also foundthat fresh detritus had 100 x 103 bacteriacel 1s mm-2 wnile ayed detritus nadonly 20-40 x 103 cells mm-2. Colonizationby microalyae (pennate diatoms, tldyel1 ated prasi nophytes, and f i 1 amentousblue-greens), however, tended to be inverselyre1 ated to bacteria density wheninorganic nutrients were limiting, suygestinythat either tne two yroups werecompeting tor the available nutrients orthat one or the other was producing inhibitory substances (Del ucca and McCracken1977).Stuart et al. (1981) conductedcontrol led experiments of heterotrophicutil ization of particulate (43-63 vm)kelp debris and found that ~t~dximuli~ bacteriabiomass (%4 my 1-1) occurred withinten days; thereafter, phayotrophic fl ayel-1 ates , ci 1 i ates, amoebae, and choanof 1 agellates successively domindted the microbialco~ru~lunity. During the initial twodays of the experiment diSS01 ved organicst'ronl the particles were used by free-livinybacteria. Over the next four daysthere was rapid growth of the bacteriapopulation attacned to the particles,with substrate carbon converted to Dacterialbiomass at a conversion efficiencyot about 33%. The following four days,unti 1 yrazi ng flagellates appeared, werecharacterized by a rapid decl ine in tnerate of bacterial yrowth, with a drop inthe conversion efticiency of approximate-bacteria ml-I of mud-water slurry) weredocumented from the sandy sediments atHarrington Point in the Columbia Kiverestuary but were much more variable thanthose in sediments beyond the influenceot the Columbia Kiver. Uudl itatively,three groups of Pseudomonas strains, a1 1nonpi ymented carbohydrate uti l i zers(Shewan 1963), comprised 85% of the bacteriaisolates identified in the estuary;the only si yni ficant non-Pseudomonasstrain found was Achromobacter, a nonpiyn~ented,nonnlotile-rod forrn. Cellulosedigestinybacteria were re1 atively uniqueto estuarine and continental shelfsediments.4.4 PHYSICAL, CHEMICAL, AND BIOLOGICALCONDITIUNINGUndoubtedly one of the most criticalrate-control 1 iny processes in the detrituspathway of an estuarine food web is theconversion of detritus to particles ofphysical dilnensi ons and nutritional characterwhich can be utilized by detritivores.Tnl s process, termed "conditioning"of the detritus, involves physical,chemical, and biological mechanisn~s (Fi y.4.2). Physical and chemical decay are dueprimarily to the weatheriny of the largercomponent of LPN particles through leachingand autolysis of soluble or volatilematerial. Physical conditioning a1 soincl udes the mechanical breakdown of cellwalls by wind, wave, and current action,which increases the rate of chemical decay.This is particularly evident inexposed, coarse substrate (e. y., cobble)1 i ttoral habitats, where continued sedimentmovement acts to break loose macrophytematerial into proyressively finerparticles (Fig. 4.3).

Fig. 4.2. Conceptual illustration of the mechanisnls and flows involved in the physical,chemical, and biological conditioning of detritus.Fig. 4.3. Terrestrial (wood chips, tree bark, and leaves) detritus of varying particlesizes deposited on 1 ittoral flats of Duckabush River estuary, Hood Canal, Washington;once degraded into finer particulate matter by physical Processes, the fine particulatedetritus is transported into blind Or subsidiary channels where further biological andchemical degradation and, ultimately, util i ration take PI ace (photo by author).43

Li tterbay experiments, wherein fresh( l i ve) macropnytes are pl aced in mesh baysand secured in littoral or marsh habitatsfor temporal monitoring of decomposition,have often been used to docunient thebreakdown of large detritus. Kistritzand Yesaki (1979) fol lowed the disappearanceof tne sedge, Carex lynybyei, in theFraser Kiver estuary. They found that 40%of the asn-free dry weight remained afterapproximately nine months (September-June)and that decay was most precipitous duringFebruary due to increased physicaldeterioration and tidal removal. ScienceApvl ications , Inc. and Woodward-ClydeConsultants (1981) conducted 1 itterbayexperi~nents using seven emergent plantsuecies (Carex lvnubvei . potenti1 la uacif-- i ;a, ~ ~ r i s t i s balticus,' - Sci r-pus validus, cespi tosa, Triofthem a Kiver estuary. They found varyiny rates of decomposition with pl dnt species,locations in the estuary, and tidalelevations, with rates varyiny from 6% to51% over five rnonths. Rates were typicallyhigher in the riverine portion of theestuary and succulent marsh plants yenera1ly decomposed lrlore rapidly than didyrasses.As much as 89% of the biomass ofparticulate kelp detritus incubated inStuart et al.'s (1981) experiments waslost in 30 days and the maximum lossoccurred in the initial 14-18 days. Thisexperiment was conducted in the absenceof any herbivorous oryani sms, which bytheir own fragmentation and ingestion ofdetri tal particles accelerate the decornpositionby increasing the surface areaavai lable for microbial colonization.Herbivores also increase the nutritionalquality of the detritus pool throuyh theaddition of nitroyen in their feces particles(Fig. 4.2).Most consumers require food sourceswith an average ratio of carbon to nitrogen

~nicrobes, and their consul~lers in estuaries lnaynitude and pdthways of nutrient andare more co~nplex than realized initially carbon recycliny within the deco~nposer-(Christian and Wetzel 1978). AS such, detritivore phase of the estuarine foodthe relative importacce of energy and web must be turther defined for differentnutrient requirements of i~iicr~bes dnd detritus sources as well as within theconsumers, the heteroyeneity of rljicrobe vdrious estudrine lldbitdts such dScolonization in time and space, and the channels.

INVEKTEBKATE ASStMBLAtiES UF t-:STUUgINE CHANNELSlnverteorate animals chardcteri sticof estuarine channel habitats are typical -1s' cateyorized by size. mi crohabitat, and1 i te hi story characteristics. Sl ze categoriesinc lude:1. Meiofauna; animals 1UU to SUU p ni, includingprimari ly foramini teraris,nematodes, kinorhynchs, ostracods,harpacticoid copepods, turbellarians,01 i yocndetes, halacarids, gastrotichs,and cephalocarideans ; and2. Macro- or meyafauna; animals largerthan 500 1~ in, including primarly polychaetes,cal anoid and cyclopoid copepods,leptost racans, mysi ds, cumaceans,tarlaids, isopods, amphipods,euphausiids, decapods, gastropods,pelecypods, and echinoderms (Mare1942; Carriker 1967).Microhabitat categories include:1. Benthic infauna; animals inhabitingthe sediment, either beneath or inthe surface of the bottom substrate;2. Sessile epifauna; animals relativelypermanently attached to the substrate;3. Motile epifauna; animals which activelymove about on the bottom;4. Epi benthic zooplankton; semiplanktonicanimals inhabiting the interfacebetween the substrate and water column,either passively or actively movingbetween the very surface layer ofthe substrate and the boundary layerof the water column; because of theemergence of many motile infaunal organismsfrom the benthos, there oftenis overlap between the benthic infaunaand epibenthic zooplankton assemblages;5. Pelagic zooplankton; planktonic ani -mals inhabiting the water column;and,6. Neuston; animals driftiny upon or immediatelyassociated with the surfacelayer of the water column.Life history categories refer primarilyto planktonic animals and include:1. Meroplankton; ternporari ly planktonicanimals, usual ly eggs and larvae ofbenthic and nektonic adults; and,2. Holoplankton; permanently planktonicanimals which live in the water columnthroughout their complete 1 i fe cycle(Sverdrup et a1 . 1942).While the following description ofestuarine channel invertebrate assembl ag -es is organized along microhabitat categories,these other descriptors wi 11 furthercategorize invertebrate fauna withintheir microhabi tats. Inclusion of characteristicorganisms in unique mi crohabi tatcategories, furthermore, is often compl i -cated by the behavior of animals and ofthe scientific apparatuses used to samplethem. Therefore, the foll owi ng descriptionsof invertebrate assemblages are- functional, in that animals are includedaccording to their occurrence in the reportedcollections, even though thei rmicrohabi tat distribution may be poorlyrepresented and considerable overlap isevident.5.1 BENTHIC INFHUNA AND SESSILE EPIFAUNADue to their permanency within orupon estuarine channel substrates, benthicinfauna and sessile epifauna are the assemblagesmost structured by variations

and yradients in physical and chetliicalcharacteristics of the benthic envi ro~sof the estuary. But, on the other hand,they exhibit the most stable structuresover time due to the assembla$e's adaptationto hiyhly variable conditions.The two factors most often cited asstructuriny the distribution of estuarinebenthic infauna are salinity and sedimentstructure (Wieser 1959; tiunter 1961,Carri ker 1967 ; Gray 1974), especial lygi ven thei r typical lonyi tudi nal yradi entstructure through most estuaries. Associatedphysical and chemical factors suchas sediment stabi 1 i ty and organic contentconstitute re1 ated influences whi ch cannotnecessari ly be separated from sedimentgrain size and texture (Sanders 1959). Thesarne holds for biological factors such ascompetition, predation, and life historycycles (Peterson 1979). But in general,and especially in the nlore dynamic channelhabitats, estuarine hydrology is theunderlyi ng, composite factor deter~itini nythe distribution of benthic infaunathrough the structuring of salinity,sediment, velocity , and oryani c matter.The role of salinity in mainstem sa~npl i ng in closely adjacent sampl inychannels has not often been correlated to sites suggest that nemerteans, nematodes,the distribution of benthic infauna in oliuochaetes. uolvchaete annelids (Macle-Pacific Northwest estuaries. Marriaye Ion; spp., ~a~iteila capitata, ~drao3"Ta.(1954) and Burt and McAl ister (1958) i l-platysvanchl a, ---. Eteone spp., - Nephthys cal i-lustrated that the gaper clam, 1 f - e ~ ~ forniensis. ~Hauloscolo~~os SDU.. Sviocapax, and softshell clam, Mya arenarig, 7-7nE; ---- -- ~enidae -m, ydt;lmarid-2~zwere distributed in sal i ni ty?nes great- phi pods (Phoxoceptial idae spp., includinger than 25°/00 between 20°/00 and OOI'~O, - Araphoxus -- -- --- . rrii -- 11 eri , and - P. stenodes,respectively.Eohaustories estuarius, E. washingtonianuC-Sj;Ebmd i urn s hoenla ker i ~ - > i i T f j ~ i eBenthic infaunal assemblages of the rnol I ;cs-b x t n m r e the dotni nan tColumbia River estuary have been sampledextensively (Columbia River Estuary DataDevelopment Program [CUEDDP] 1980), particularlyin reference to the effects ofdredging and dredge-materi a1 disposalwithin and immediately adjacent to theestuary (Sanborn 1975; ~igley et al.1976; Ourkin et a]. 1979; Higley andHal ton 1978; Bl ahm 1979). It wasnot until the initiation of the CKEODPstudies that detailed synoptic and ecol0yical investiyations of benthic infaunalassemblages were conducted throughoutthe estuary (Oregon State UniversitySchool of Oceanography 1930a). At theinitiation ot the CKEDUP studies, a compositespecies checklist of the estuary'sinfauna included 212 taxa; 23-f whict)were polychaete annelids; 14"/,amnlaridatllphipods; 9% bivalve molluscs; and 8%eacti, gastropod rriol luscs and isopods(VTN, unpublished, cited in Oreyon StateUniversity School of Ocednography 1980a).Unfortunately, only a few of theCKEDllP benthic i nfauna sa~npl iny stationsare located in channel habitats and infor-Illation from these stations is as yet incomplete.However, the combined studiesof the Columbia Kiver estuary, culminatingwl th the on-going CHE[)DP research, sti 11present the niost comprehensi ve i 11 ustrationot bentnic infauna in estuarine channelhabitats of the region (Fox 1981).H diverse, low standing stock, intaunalassenibl aye typifies tne region atand immediately within the mouth of theColumbia Kiver estuary in a benthic environ~~lent characterized by l arye-yrained,unstable sand substrate of low organlccontent and high salinities. While notrue channel habitats have been sampled,intauna w~Tiii?i-TnK'I~- total derlsity ofthe assemblage ranges between 200 to 1000individuals m-2 (Hiyley and Holton 1978;Oregon State University Scf~ool of Oceanoyraphy1980a; K. Holton and D. Hiyley,Oregon State Ilniversi ty , unpuol ishedCgEUDP data).Uentnic infauna in the central reyionand principal mlxing zone of theColumbia Hi ver estuary i 1 lustrate extre~~~espatial and tetr~poral variability, evenwl thin distlnyuishable habitats such asthe channels. As described in Chapter 2,

salinities are highly variable (5"/,,-25O/,,) and the sediment (medi um sand)prone to resuspensi on and di f ferenti a1 ,active transport. Gammarid amphi pods(Corophium salmoni s , Eoyammarus confer-vi cot us, E. estuarius) , 01 i yochaetes,m e t e -annelids yci nde armi gera,Magel ona sacculata, Polydora s;. , Paraone1- 1 a pl atybranchi a, Hobsonia florida,~eant nessp.),andcuma~~emil~nm o m i n a t e the infaunal assemblagewithin or closely adjacent to channels,and the total assemblage can sustain hiyhdensities (20,000-70,000 m-2; Higley etal. 1976; K. Holton and U. Hiyley, UregonState Univ., unpublished CREDDP data).The benthic infauna assemblage ofthe subsidiary channel enteriny the mixing zone region from the Lewis and Clarkand the Youngs Rivers through Youngs Baybest illustrates the synergistic influenceof the fine sediments (fine sand tocoarse silt) and high sediment organics,despite relatively high current velocityregimes (Uoley et a1. 1975). Tube-buildinygamrnarid amphi pods (C. salmonis),polychaete annelids (ti. florida, Neantheslimnicola), bivalve m s l u m balthica,Carbicula manilensis), oligofiaetes, and--chi ronimid 1 arvae dominated the finer sub-strates. 01 i gochaetes dominated numeri -cal ly over Corophium in the very fine,hi yhly-organ? c sediments and other amphipods(E. estuari s, Ani sogammarus marussp. , xraphoxus sp. ) replaced Corophiumin the coarser, less organic sedimentscloser to the mainstem channel in the centralportion of the estuary (Higley andHolton 1975). Total densities of benthicinfauna in the inner-bay channels exceeded30,000 m-2 but were only 323 m-2 intne outer-bay portion of the channel (Higleyand Holton 1975). Specifically, C.salmonis occurred in densities between--19,000 and 29,000 nr2- 01 i gochaetes, indensities between 5,006 and 33,000 m-2-and polychaetes, between 600 and 2,200 m-2in the fine sediment channel bottomhabitats.Channels in the upper estuarine andriverine regions of the estuary includeboth the mainstem, navigation channel andsubsidiary channels in the complex is1 and-tidal marsh habitats where salinities arelow to absent and sediments are typicallycoarse (medi um sand). Gammarid amphi pods(C. salinoni s, Monoculodes spi nipes,PTioxocepnal idae spp:), polychaete annelids(N. limnicola), ol igochaetes, bivalvemolluscs(C.manilensis), and chironomid1 arvae are-representati ve benthic oryanismsin this region. Total densities tendto be low,

Fig. 5.1. Representative illustration of common benthic infauna and sessile epifaunaassembl ages of estuarine channel habitats of the Pacific Northwest.frequently dredyed channels in the up- or 1971). The polychaete annel~d, Q-stream portion of the estuary. Elsewhere, cinde armiyera, and gaper clam, Tresuschannel habitats have been studied on a capax, were the predominant infaunalmore 1 imi ted oasis. Mai nstem channels in macroinvertebrates in the less-scouredthe lower, marine-influenced region of channel bottom ot the South Slough por-Coos Bay, Oregon are characterized by tion ot Coos Bay (Hancock et al. 1977).coarse-yrai ned, ocean-deri ved sand in thebottom sediments and steep, mudstone wallsUndoubtedly the most complete quanwherea navigation channel was created. titative characterization ot benthic in-The unconsolidated bottom sediments are fauna in dendri tic channe Is of estuarinecharacterized by the polychaete annelidssalt marshes (tidal creeks) in the regionOphelia limiena, Nephthys spp., and is that of Siletz and Netarts Bays,Typosyll is fasciata, while the consolidat- Oregon by Hi gley and Holton (1981). Theyed mudstone walls harbor burrowing pelecy- found that 01 igochaetes numerical ly domi -pods or piddocks, Pholadidea (Penitella) nated the macroinvertebrate assemblage,Penita (Jefferts 1977; Hancock et al. accounting for approximately 50% and 70%197f),' Sessile organisms on the channel in mature hiyh marsh and sedye marshwall include the mussels Myti lus edulis tidal channels, respectively; polychaeteand Modiolus modiolus; encrusting sponges, annelids and amphi pods often accountedHal iclona spp. ; bryzoans, Bowerbankia for over lo%, and nematodes, dipteransp. ; hydroids, Tubularia marina; and the 1 arvae, cumaceans, and harpacticoidanemone, M e t r i d i m ~ . S . ~ . Interi- coyepods were somewhat less abundant.49

Table 5.1. Itemization and characteristics of benthic infauna and sessile epifaunacomnon to estuarine channel habitats of the Pacific Northwest.~ aiiii l ty Sediment Re1 evant Li f

_I_llll__l_______l_____l_l_l____-I_------I-TaxaUIVALVE MOLLUSCS - cont 'd.-- Modiolus modiolusMacanla - - - .... bal . thi ca-- Crobicula manilensisProtothaca -- stanli neaSaxidonlus yi yanteus --- Tresus - capaxPhol adidea peni taZ i r f a eaTjislETi-Tab1 e 5.1 Concl u.fetl.-~ ainlty l Sediment Relevant Li feCtrannel Associ - ASSOC~ - Hi story Char-~abi tats1 ations2 ations3 ------------- acteri sticsME, PM, S ,U t,Ps, 6 K-UM,Sk,PM,SE,PM,SE,PM,SE,DI4 k ,PSH-ETHNAIDSTanais sp.UM-PGAMMAK ID AMPH I PODSAlnphi thoe spp.Corophiurn spp.-- Ani souralrlnlarus su.~o~amiarus confervi col US ---- Eohaustorius estuarius- ~onoculodesspi nipesPhoxocephalidaeParaphoxus spp.S, U K-PS ,UH-PSM-PM,SPM, S M-ESU-MTubedwellersDIPTERAN INSECTSChi ronomidae U R-P Sc Larvae,pupae1~ = mainstem; S = subsidiary; U = blind.2~ = riverine; O = oligohaline; M = mesohaline; P = polyhaline; E =euhaljne.~ S C = silt/clay; S = sand; 6 = yravel; C = cobble; B = boulder; Cn =consolidated.Amony the arnphipods, Corophlum spp. SIJ~J.) were corrllnon but not abundant in thecomprised about YO"/,f the total number nlature hlyh marsh channel. The small telinboth marshes, with Anisogammarus -linid, --- Macoma -- balthica, was also relat~ve-- confervicolus contributing up to 10% in ly colllmon In the seGe channel but not inthe sedye marsh and taiitrids and Amphi- the mature high nlarsh channel. rota1 denthoespp. also occurring in the mature sities were also appreciably hiyher7-h~yh marsh. Capitellids accounted for (202,205 W2) in the sedye marsh channelmost (59%-75%) of the numbers of poly- than in the mature high ~narsh (38,238chaetes in both marsh habitats, hut Hob- Ine2), a density disparity which could besonia florida was also prevalent (>20"/.1 n the sedye marsh channel, and ampharetprimarily attrlbuted to a nine-told higherdensity ot polychaetes in the sedge marshids, spi robids, and spionids (Streblospio channel. While the meiofaunal component5 1

of these dendritic marsh channels has not Uurkin (1Y73), and Kujala (1975) qualitabeenwell documented, it would appear tively described the riverine distributionthat in general the infaunal invertebrate of the crayfish Paci fastacus leniusculus,assemblages in these high-elevation chan- the oligohal ine-euhal ine distribution ofnel s are of significantly lower diversity immature sand shrimp, Crangon franciscorthanthey are in lower-el evation, subsidi- - um f ranciscorum, the mesohaline-euhal ineary and mainstem channels even though the distribution of Ounyeness crab, Cancerstanding stock may not be significantly magister, and the euhal ine distributiondifferent. o fcauda.t C. franciscorum and C. nigri-Det2i led bio-1 basen ne stud-Altnouyh considerable variability ies by Higley and Holton (1975) and Higley[nay exist between assemblages character- et al. (1979) in the Youngs Bay (mesohalizing coastal and "inland" estuary com- ine-polyhal i ne) reyion of the estuary docylexesot Puget Sound and the Straits of umented the seasonal variation in theGeorgia and Juan de Fuca, comprehensive abundance of C. tranciscorum. Mo reintonnation on channel infauna in the detailed tempor4 and spatial documentalatterestuaries is generally lacking. tion of the standing stock of C. francis-Benthic organisms dominating sandy sedi- - corum and C. magister has since been~ilents of a blind channel in a Scirpus proauted by -the CKEDDP studies (tioughtonmarsh in Puget Sound included t h e m et al. 1980; Fox 1981).chaete Manayunkia aestuari na (maximummean density %4 x 10-1igOchaetes( ~ 2 x 105 m-2), the gammarid amphi pod Cons01 idated, these studies repre-Corophiuln salmonis ($1 x 1u5 W2), the sent a relatively cohesive picture of thetanaid ~ana-sp.1 x lo5 w2), and the cot~lposition of the motile epifauna in theb1vdlveMacorna balthica ( sp. 2 x 103 me2) Columbia Kiver estuary. Althouyh sampl iny(J.E. Srnitll98Ome these densities for P. leniusenlus has been neither efappearnigher than those reported in the fective nor extensive, subsidiary channelsotner studies, the ditteriny sieve mesh in the riverine and upper oligohaline resizesutilized in these studies preclude gions of the estuary appear to harbor modanydirect comparisons.erate densities of this crayfish; occurrencesand densities in mai nstern channel s5.2 MOTILE EPIFAUNA and channel slopes is low, however, andsuggests that the principal location ofMotile epifauna, due to their con- these populations is in the littoral orspicuousness or commercial importance, shallow sub1 i ttoral habitats. At thetend to be more extensively documented marine end of the estuary, juvenile Dunthaneither infauna or zooplankton. All geness crab and adult C. niyricauda andare essentially macroinvertebrates which - C. alaskaensi s appear 30 be 1 imi ted tohave the ability to control their move- euhaline water masses in the channels, almentalong the bottom. Some actually en- though Dunyeness crab were reported withterthe water column during some periods in the lower (seaward) polyhaline reyion(e.g., at night) and, as such, constitute duriny summer low-flow periods. Fewthe macroinvertebrate component of the mature or gravid Dungeness crab are foundestuary's nekton assemblages at these within the estuary, suggesting that thesetimes.moti 1 e macroinvertebrates are moving intothe estuary from spawning populationsAs in the case of benthic infauna, located outside tne mouth of the estuary.information from the Columbia River estu- Crangon franciscorum represents the trulyary provides one of the most comprehen- endemic estuarine macroinvertebrate, parsivepictures of motile epifauna in chan- ticularly during the early stanzas of itsnel habitats of coastal estuaries life history. Adult sand shrimp appear(Columbia River Estuary Data Develo~ment to reproduce in the euhal ine regionsPrograrll 1980; Houyhton et al, 1980; Fox during winter and depart the estuary by1981). Haertel and Osterbery (1967), mid-spri ng. Juveni le sand shrimp remain52

and rear within tne estuary, predominantlyin rnudflat, sandflat and slope habitatsbut also in channels. The distributionof these populations gradually expands upthe estuary with the intrusion of niesoandpolyhaline waters duriny low freshwaterflow through the summer months.Similar distributions and life historypatterns of Crangon have been describedfor other coastal estuaries in Ureyon(Kryyier and Horton 1975).In 1971) tne mean total density andstandiny crop of the motile epi faunalassemblage in the channels of the ColumbiaRiver estuary ranged between 0.03 and0.26 individuals m-2 and 0.03 and 1.21 gm-2, respectively.Earl ier quantitative investi yationsof Uungeness crab in Humboldt Bay (Gotsnall1978) indicated that densities ofcrab in that large coastal estuary aresignificantly higher than in the ColumbiaRiver or Grays Harbor, which may be relatedto the more euhal ine-polyhal ine conditionsin an estuary with such low riverineoutflow. Demersal trawl catchesindicated maxima as high as 0.5 m-2 inwinter, 73% of which were O t year age recruits;the annual mean averaye crabdensity from trawl catches was estimatedat 0.09 m-2 (actual density estimates byArmstrong et al. 1982). Underwater SCUBAsurveys, however, indicated that crabswere actually more dense, averaging 0.11m-2, in August and September. Given thebehavior of Dungeness crabs to burrow intosediment (MacKay 1942), seasonal andshort-term variability in density estimatesbased upon net catches may be attributableto the various factors influencing the proportion of the popul ationwhich is buried (i.e., mating, spawniny,feeding, exposure during low tides, lowsalinities).Extensive investigations of Dungenesscrab and crangonid shrimp in GraysHarbor have been recently compl eted(Armstrong et al. 1982) and provide themost detailed information available oncrab and shrimp abundances, movenients,population dynamics and food web relationsnipsin estuarine channel habitats.Meyalops larvae of Dunyeness crab appearedto have entered Grays Harbor fromoceanic habitats in spring and began tometamorphose and settle in benthic habitatsin the outer (euhaline-polyhaline)regions of the estuary. Juvenile crabsof the 0+ year age yroup (recruits) wereconcentrated in mudfl at and adjacentchannel habitats. The 1+ year age yroupwas more abundant and distributed throughoutthe estuary. The 2+ year age groupwere less abundant than the 1t year agegroup but more abundant than the 0t yearage group and were distributed predominantlyin the outer region of the estuary.The 3+ year-old crabs were relativelyrare and occurred only at stations closeto the mouth of the estuary. Mean crabdensity ranged from 0.076 crabs rn-2 to0.012 m-2 and general ly decreased withincreasing distance up (upriver) theestuary in response to decreasing bottomsalinity. Densities in the outer estuary(0.051 m-2) were significantly yreaterthan densities in the upper region of theestuary (0.030 m-2) and the same was truefor the period of March-Auyust (0.048 m-2)compared to the period of September-February(0.021 m-2). Considerable movementbetween channel and shal lower habitatsalso occurred as a possible result of tidalinundation and dewateriny of littoralhabitats and as a result of die1 foragingbehavior. The consequence of these activitypatterns was that the crabs were foundrelatively congregated in channel habitatsduriny day1 i yht low tide periods. Furtherconcentration of crabs in channel habitatswas also attributed to the effects of reducedsalinities in the shallower habitatsduring periods of high riveroutflow.Qua1 i tati ve summaries of motile epifaunain other coastal estuaries (Monroeet al. 1974; Percy et al. 1974; Kreag1979a, b, c; Ratti 1979a, b; Roye 1979;Starr 1979a, b) further indicate thatDunyeness crab uti 1 i ze estuarine channelsto varyi ny degrees, principally dependingupon the volume and spatial extent ofeuhaline and polyhaline water masses inthe estuary. While most estuaries appearto resemble the Columbia River estuary inthe limited distribution of juvenile

crabs and scarsity of adult crabs, Coosand Tillamook Bays, with their greaterproportional extent of euhal ine and polyhalineregions appear to maintain adultpopulations in the lower reaches and havejuvenile crab populations distributedfurther up the estuary than the others.Simil arly , Dungeness crab populations inthe "i nl and" estuaries of Puget Sound andthe Straits of Georgia and Juan de Fucaare endemic throughout the year, althoughthe moved lower in the estuary's channelsduriny spring and other high freshwaterflow periods.Three species of crangonid shrimps,Cranqon f ranciscorum franciscorurn. C.nigricauda, and C. stylirostris, * werefound to predominate in Grays Harbor(Armstrong et al. 1982). C. franciscorumwas prevalent throughout -the estuary,while C. nigricauda and C, stylirostriswere c-on only in outerreaches of theestuary; the differential distribution of- C. nigricauda and C, stylirostris wasattributed to lower filerance to low bottomsalinities and some form of competitionwith C. franciscorurn. The densitydistribution of C. franci scorum showedstrong seasonal pFtterns, with peak densitiesas high as 5 individuals m-2 occurringthe @per reaches of the estuaryin spring through summer. Shrimp densitiesin the outer reaches of the estuarywere siyni ticantly lower (0.3-0.9 rn-2)and typically illustrated earlier seasonalmaxima than occurred in the upperestuary. Observed die1 fluctuations inshrimp density in a littoral flat habitatin the outer estuary was interpreted as anight-time habitation of shallow habitatsfor the purpose of teeding and movementinto channel habitats during day1 i yht inorder to decrease vul nerabi 1 i ty topredation.In one of the few studies includingmoti 1 e macroinvertebrates in channel habi -tats of estuaries inside the Strait ofJuan de Fuca, Northcote et al. (1976)described the distribution and standi ngcrop of Cran90n franciscorum through 150km of t h e m ~ r a s e River r and its estuary.Unlike its occurrence in the coastalestuaries, however, C. f-ranciscorum wasnot found beyond the polyhal ine region ofthe estuary which is restricted to thelower 10 km of the North and Main ArmsChannel s.A generalized i 1 lustration and characterizationof moti le epi fauna common toestuarine channel habitats of the PacificNorthwest are presented in Fig. 5.2 andTable 5.2.5.3 EP IBENTHIC ZOOPLANKTONThe least understood component ofestuarine communities, particul arly withinchannel habitats, is that of the epibenthic zoopl ankters which occupy theboundary zone between the bottom substrateand the water column. Increasedappreciation of their role in transferringdetrital carbon to higher trophiclevels (Kaczynski et al. 1973; Chang andParsons 1975; Sibert 1979; Simenstad etal. 1979a). however, has recently sponsoredinvestigations focused upon thestructure, standing stock, behavior, andfood web relationships of these assemblagesor component taxa.Initially, studies of epibenthic zooplanktontended to be either specifical lyoriented toward prominent macrofaunaltaxa such as amphipods and mysids (Chang1975; Davis and Holton 1976; Davis 1978;Levinys 1980a; Pomeroy and Levings 1980)or, if assembl age-oriented, have by vi r-tue of the collecting apparatuses beenefficient only with macrofauna (Haerteland Osterberg 1967). Consequently, documentationof epibenthic meiotauna, especially f rorn quantitative or assemblageorientedstudies, has appeared relativelyrecently (Crandell 1967; Higley and Hol ton1975; Kask and Sibert 1976; Sibert et al.1977b; Simenstad et al. 1979a, 1980;Houghton et al. 1980; Sibert 1981). Ofthese studies, however, only the CREDDPstudies in the Columbia River estuary(Houghton et al. 1980) have provided aholistic, quantitative description of epibenthicmeiofauna assemblages in estuarinechannel habitats. A generalized il lustrationand characterization of epibenthiczoopl ankton common to estuarine habitats

--Pisaster ochraceousFig. 5.2. Representative i 11 ustration of comr;ion motile epifauna assemblages of estuarinechannels of the Pacific Northwest.of the Pacific Northwest are presented inFig. 5.3 and Table 5.3.In conjunction with pump sampling ofepi benthic zooplankton at eleven littoraland shallow sublittoral sites in theColumbia River estuary, Houyhton et al.(1980) and Simenstad (Fish. Res. Inst.,Univ. Wash., unpubl. data) documented theresults of epibenthic sled sampling infour channel sites distributed within theestuary between Apri 1 1980 and February1981. Over that period, epibenthic zooplanktondensity estimates in the channelsaveraged 6.7 x 104 organisms m-3 (definedas 0.5 m over the bottom) and ranged be-tween 615 m-3 and 6.7 x 105 m-3; standingcrop averayed 1.02 g but ranged ashigh as 11.5 g m-3. Almost two hundredseparate taxonomi c/l i fe hi story stagecateyories were identified from the assemblage. The cal anoid copepod Eurytemoraaffinis and undifferentiated coyepodnaupl i dominated the composition basedon density, comprising 30.5% and 17.8% ofthe total number of organisms, respectively.There is a major question, however,whether either Eurytemora or copepodnaupl ii should be considered as epibenthicorganisms since they may occur closeto the bottom merely as a result of entrainmentin the deeper, more saline watermasses. Of the true epibenthic fauna,ectinosomatid harpacticoids (13.7%), andthe cannel lid harpacticoid Scottol anacanddens i s (9.5%) predominated nmerical~ly. Eurytemora a1 so dominated (31.9%) thestand% crop, followed by Crangon franciscorum(18.4%); among the true epibenthiczoopl ankton, Neomysis mercedis(6.7%), Scottol ana canadensi s (5.-Corophium sal moni s (4.6%) predominatedthe composi tion gravimetrical ly. Standingstock of epibenthic organisms as measured

Table 5.2. Itemization and characteristics of motile epifauna common to estuarinechannel habitats of the Pacific Northwest.---Re1 evantLifeSal ini ty Sediment Hi storyChannel Associ- Associ- Character-Taxa ~abitatl ations2 at ions3 istics4ECHI NODEKMSPi saster ochraceousPycnopodia he1 ianthoidesDECAPODSPacifi castacus 1 eni uscul us s,B R SC F-EDCrangon a1 askensi s M P-E s,G 0-MCC . c i scorum- -- M,S,B 0- E S,G 0-MC; onlyjuveni 1 esextend into01 i gohal i neM E S, ti 0-MCM Cn ,B F-EDM,S M-E S,G F-BC ;Appearprincipal 1 yas juveniles- C . y roductus- ---- M,S M-E SC ,S F-BC1~ = mainstem; S = subsidiary; B = blind.2~ = riverine; 0 = oligohaline; M = mesohaline; P = polyhaline; E =euhal ine.3~~ = siltlclay; S = sand; ti = gravel; C = cobble; B = Boulder; Cn =consolidated.40- = obligate; F- = facultative; BC = benthic carnivore; ED = epibenthicdetritivore; MC = meiofauna carnivore.by the sled in 1980 generally increasedbetween Apri 1 and May, declined in ~une,3increased again in July and August, anddecl ined between October and February1981. Peak mean standing stock typicallyoccurred in the estuarine mixing (mesohaline)region of the estuary. This phenomenoncould be attributed to either physicalentrainment of the zooplankters withinthe nu1 1 zone or increased production anddiversity of zooplankton assemblages due3~ampl ing immediately fol lowed theMay 18 eruption of Mount St, Helens andthe resulting influx of turbid freshwaterinto the estuary.to the accumulation of detrital food resourcesby settl ing and flocculation (seeSection 4.2). Houghton et a1 . (1980) concludedthat epibenthic zooplankton assemblagesin the Columbia River estuary couldbe partitioned into the three basic assemblagesdescribed by Haertel and Osterberg(1967): 1) a riverine assemblage whichis primarily a product of the freshwaterColumbia River ecosystem above the estuary,2) a euryhaline, mixing zone assemblage of indi genous estuarine species,and 3) a marine assemblage, much of whichis contributed by the tidal intrusion ofoceanic water through the mouth of theestuary. Some prominent taxa such as the5 6

HBIBcflnosoma spp' ' AcanlhMnys~s spp . 'ArChaeOmySlS grebnifakrl'Fig. 5.3. Representative ill ustration of common epibenthic zooplankton assemblages of-.-L ..-.- :- -L---.-_T L _ L _ . ~ _ ~ - -.E n--:z:- rt,....ch ., +ectinosomatids and Scottolana canadensis,however, are distributed ubiquitouslythroughout the estuary, even upstream inthe riverine region.Crandell (1967) also employed an epibenthicsled (Cl ark-Bumpus) and describedthi rty-two taxa of epibenthic harpacticoidand cyclopoid copepods in the channelhabitats of Yaqui na Bay, Oregon. A1 thoughthe sled samples were not considered quantitative, based simply on occurrence, theprominent harpacticoid taxa included Tis--.be furcata, Microarthridion 1 i ttorale,x-phiascel la &bil i s, Canuel la (= Scots1 ana : Coul 1 m a n a d e n s i s , parathalestris.- sp. and ~chizopera sp., and the cyclopoidcopepod Ascomyzon latum. Crandellconcluded that the epibenthic fauna in thechannels during the winter were derivedprimarily from mudflat assemblages butthat an endemic channel assemblage domi-nated by Tisbe furcata had developed byfa1 1 ; thi s x e - pattern was re1 atedto lower water temperatures in thefall and an extended period of relativelyhigh bottom sal ini ties which enabled moremarine forms to enter the bay via thechannel s.While the structure and standingstock of the channel assemblages of epibenthiczooplankton in the Columbia Riverand Yaquina Bay estuaries i 1 lustrated considerabletemporal and spatial variation,no effort was expended to quantitativelyestablish the relative role of biotic (reproduction,recruitment, growth, selectivepredation) and abiotic (salinity,temperature, current velocities, sedimentsize, structure, and organic content) factorsin accounting for the direction ormagnitude of the variation. Williams(1983) step-wise mu1 tiple regression

Table 5.3. Itemization and characteristics of epibenthic zooplankton common to estuarinechannel habitats of the Pacific Northwest.TaxaRe1 evant Li feChannel~abi tats1Salinity Sediment~ssociations ~ssoci at ions3History CharacteristicsROTIFEKABrachionus spp.Asplanchna spp.CRUSTACEACLADOCERADiaphanosoma brachyururn?- spp*id%2$%as!ip.Bosmina sp.Evadne nordmanniPodon spp.Alona spp.Chydorus spp.Leydi gia spp.R-0R-MRR-0R-0P-ER-UR-EH-0ROSTRACOUALimnocythere sp.COPEPODACALANOIDAEurytemora affinisDi aotomus - soo.-rr-Acartia spp.HARPACTICO IDAScottolana canadensi sEctinosornatidaeMi croarthridion 1 ittoraleTachidius spp.Laophont i daeParaleptastacus sp,Nitocra SD.~untemann; a jadensisBryocamptus sp.BUI bam~hizcus sp.Ha 1 ect i nosoma s p.R-ER-E0-EM, S R-EM,SR-EM,SK-EM7SMK-ER-EMEMM-EM 0-EM -EMR-PM,SM-ESYBP-ES 9 BM-BP-E0-ESM-ESM-EMPSM-EM ,SM-E(continued)58SC-GNNSSSC-SSSSSSSSS-GSCSCSC-SSSSS

I___---Table 5.3. Concluded.Relevant LifeTaxaChannel~abitatslSalinity Sediment History Char-~ssociations ~sso~i~tions3 acteristicsCYCLOPOIDACorycaeus spp.Cyclops spp.Oithona spp.Cycl opi na spp.MY S I DACEAAcanthomysis spp.Neomvs i s mercedi s- N. integerArchaeomysis grebnitakiiHolmsiel 1 a anomal aM R-E NM R-E NM M- E NM ,S P-E SCM-SM-SM- SM-SSP-ER -EP-EP-EP-ESC-GSC-GSC-GSC-GS CCUMACEALamprops spp.Leucon sp.Leptostyl is pacificaCumel 1 a vul garisSM-SS5-BP-EEP-ESC-SAMPHIPODACorophium salmonis M- B 0-P SC-SC. spinicorne M- i3 0-P SC-SAnisogammarus sp. M- B 0-P SC-Gconfervicolus M-B 0-E SC-G- M- S 0- E SC-GEohaustorius sp. M-S 0-E SI SOPODAGnorimosphaeroma oreyonensi s M- B 0- E S-BMunna spp. S ESC-S------1~ = mainstem; S = subsidiary; B = blind.2~ = riverine; 0 = oligohaline; M = mesohaline; P = polyhaline; E = euhaline.~ S C = silt/clay; S = sand; G = gravel; C = cobble; B = boulder; Cn = consolidated;N = no definitive sediment as~ociation.analyses of the 1980 CKEDUP epibenthic organisms data, however, provided a prel imi -nary indication that taxonomic correlationsmay be more important than physicalfactors in explaining the variation inorgani sin densities. Neomysis mercedi sdensities were highly correlated withCrangon franci scorum densities; Scotto-W n a d e n s i s with ectinosomatid harpacticoid,Eurytemora affi nis, and CyclopsSpp. densities; and Cyclops SPp. highlysignificantly carrel ated with Crangonf ranci scorum, Neomysis mercedi s, andScottolana canadensis. Physical factors,on the other hand, provided only weak correlations,i .e., Cyclops spp. with tidalelevation and salinity, Scottolana canadensiswith tidal elevation and s u z ewater temperature, and ectinosomatid harpacticoidswith tidal elevation and date.Thus, while physical factors such as salinityapparently influence the distributionof epibenthic zooplankton taxathrough the estuary, the standing stock

Structure ot the various assemblages rnay velocities indicated that positive thigmobemore the result of the distribution of taxis, especially in daytime under no curfoodresources, theoretical ly detritus, rent flow, was over1 apped with positiveand carnivores on meiofauna. rheotaxis underthat behavioralcurrent conditions suchcompensation for down-Studies of epibenthic zooplankton in stream drift could occur up to 5-10 cmestuaries within the Straits of Juan deFuca and Georgia and Puget Sound have gensec-1velocities. This and data from similarstudies in the Squamish estuaryerally focused more upon their functional (Levings 1973) indicated that epibenthicrole, particularly as prey of juvenilesalmonids, than upon community structureamphipods were likely to be washed out ofthe estuary at higher current velocities.within the estuaries. Nortncote et al.(1976) sampled epi benthic macroinvertebrates(>1 mm) in shallow sublittoral,slope, and channel habitats along 150 kmof the Fraser River estuary and lowerLevings (1980b) further examined thevertical distribution and abundance ofriver. Maximum density ('~100 m-2) and epibenthos in channel habitats of the lowstandingcrop (s5UO my m-2) occurred in er Fraser River estuary and illustratedthe North and Main Arms regions of the that E. confervicolus was more abundantestuary. In most cases, comparisons ot in the-bottom drift net and pump samples,density and standing crop in the three where densities as high as 65 m-3 weredeptn habitats i 1 lustrated sharp decreas- reached.es with increasiny depth. Average taxadiversity tended to increase upriver andto be lowest at depths over 6 rn. Uominantepi benthic zooplankton taxa includedExtensive sampling of meiofauna in arnysids (Neomysis mercedi s, Acanthomysi s subsidiary tidal channel of the Nanaimospp.); dipteran and other insect larvae; River estuary has been conducted as partand amphipods ( Eogammarus confervicolus, of a joint study of the prey resources ofCorophium spp.). Euryhal ine species such juvenile salmon in the estuary (Kask andas 1. ~nercedis and I. confervicolus ex- Sibert 1976; Sibert et al. 1977a; Siberttended 40 km up the estuary while dip- 1979; Sibert 1981). While the earliestteran and other insect larvae decreased study involved benthic core sampling ofmarkedly between the lower mainstem and the meiofauna, 1 ater studies specificallyestuarine stations. Benthic oligochaetes attempted to sample only epibenthic formsand moti le epifauna (Cranyon f ranciscor- more representative of the prey assemum;see Section 5.2) -so dominant blage available to foraging fish, either-components of these epi benthic sampl es. utilizing an epibenthic sled (Sibert etal. 1977a) or pump (Sibert 1981). UsingThe distribution, abundance, and a diver-operated sled, Si bert et al.behavior of epibenthic isopods (Gnorimo- (1977a) described average epibenthic harsphaeromaoreyonensis) and amphipods pacticoid copepod densities of 9,240 m-3w m spini corne, Eoyammarus (Ani so- which, a1 though quite substantial, wereg ~ ~ c o n f e r v i c o l were u s ~ inclutredn sti 11 often orders of mayni tude less than-and Chany's (1977) studies of the densities measured by comparable coreinfluence of current vel oci ties upon the sampl es. Structure of the sl ed-capturedbenthos of the Fraser Ri ver estuary. They harpacticoid assemblage was numericallydocumented that the abundance of epiben- dominated by ectinosomids, Tachidius disthiccrustaceans collected in drift bay cipes, Parastenhelia hornel 1 i , and H z -samplers appeared to be affected by cur- emannia jadensis; Harpacticus sp., f-isberent velocities, with maximum abundances sp. and Heterolaophonte 1 i ttoral is alsooccurring in side channels with lower cur- occurred frequently in the sled samplesrent velocities, Associated laboratory but were not well represented in the corestudies of the activity patterns of E. samples, suggesting that these are trueconfervicol us under di fferent currefit epibenthic forms.60

Further definition of the structureand die1 fluctuations of epibenthic zooplanktonwas accomplished using an epibentnicpump with intakes located within5 cin and 30 cm of the sediment surface.These experiments i 11 ustrdted that, despitehomogeneous water characteristics,significantly (2x to 20x) and persistentlyhigher densities occurred 5 cm fromthe bottom than 30 cm above it. Haroacticoid(i.e.., Harpacticus Septentrional is(= H. uni remis), Microarthridion lity-torare, ectinosomi ds , -- Dac ty l opSGcrassipes, Tisbe spp.) , cal anoid (Eurytemorahirundoides) , and cycl opoid cope-W(0ithona sp.) formed the major taxai n the assembl aqe. Harpactico ids averaaedbetween 32 ani 330 in the higierdepth strata and 370 to 2,800 m-3 in thelower strata. Thus, these epibenthic or"hyperbenthi c" (Beyer 1958; Hesthagen1973) assemblages could originate fromboth upward rl~ovement of surface-dwell i ngbenthic species (Bell and Sherman 1980)and downward movement of planktonicspecies. A1 though the comparable rolesof active migration and passive diffusionare unknown, Sibert (1981) suggestedthat hyperbenthic populations originatefrom both sinking plankton and scouredmeiofauna which are physically entrainedin the turbulent boundary layer. It wasalso suggested that such entrainment maybe advantageous to the hyperbenthicoryani sms from the standpoint of hi yherconcentrations of food particles trappedwithin the turbulent layer. Given thephysical parameters determining the conditionspromoting equi 1 ibri um betweensinking and turbulent mixing (frictionaldrag velocity, particle diffusion coefficient,and current velocity), the spatialdimensions of hyperbenthi c populationswithin various estuarine habitats and thetemporal pattern of turbulent 1 ayer formationand persistence over tidal cyclesare likely to be highly variable. Unfortunately,such detai 1 ed data and analysesare not avai 1 able.While considerable sampling of epibenthiczoopl ankton has been conductedwithin the Strait of Juan de Fuca andPuget Sound (Simenstad et a1. 1979b;Simenstad et al. 198U), very little hasoccurred in estuarine ~nannel habitats.Blaylock and tioughton (1981) utilized thesaw eqibenthic plankton pump used in theCREDOP studies on the Columbia Riverestuary (tioughton et al. 1980) to sampleepi benthic assemblages in CommencementBay. Although cluster analysis of thecombined 1 i ttoral and sub1 i ttoral , estuarineand inarine saniples did not illustratedistinct epibenthic zooplankton assemblagesassociated with estuarine channelsites, the epibenthic assemblages in theblind (waterway) channels tended to beless diverse than the more marine or themid-1 i ttoral si tes, While the harpacticoidcopepod assemblages were not describedtaxonoini cal ly by site, qua1 itativeassessment of the samples has indicatedthat Ti sbe spp. , Typhlamphiascus- ifer, and Hhynchotnalestrisspy were dominant taxa in theeplbenthic habitats of the channels (J.Cordel 1, Univ. Washington, personal communication).Corophium spp. was the onlyprevalent gammarid amphi pod; Microcalanussp. and Paracalanus sp. were prominentcalanoid c m o r y c a e u s spp. and Cyclopinasp. were the most common cycEpoidcopeyods; and Cumella vul aris wasthe dominant curnacean in t e channelassemblages.+-Simenstad and Cordell (1980) alsodescribed the composition and density ofepibenthic organisms co1 lected at the endof a blind channel (City Waterway) in CommencementBay wi th the epi benthi c sled describedby Sibert et al. (1977a). Amongthe true epi benthic zoopl ankters capturedby the sled (as the sled skimmed the surfacesediments, the majority of the organismscaptured were benthic nematodes andpolychaete annelids), a low diversityassemblage of haroacticoid copepods wasprominent. ~ulba~~hiascus sp.' and Mesochcra1 i 11 jeborgi constituted the s-nant harpacticoid cope~ods and Tisbe sp.was abundant at seve'ral sites. T e r a i ldensity of epibenthic organisms within 10cm of the bottom was estimated to average42,020 m-3 and standiny crop 1.1 g nr3.A1 though these diverse studies ofepibenthic zoopl ankton were neither systematicnor Synoptic with regard to estu-

arine habitats, it 5 s evident that muchvariation in structure and standing cropwithin estuarine channel habitats exists.In cases such as bl ind, fine sedimentchannels with organic enrichment, thereis evidence for dramatically differentassembl ayes from more euryhal i ne, coarsersediment channels .5.4 PELAGIC ZOOPLANKTON AND NEUSTONPelagic estuari ne zooplankton andneuston originate from three generalsources (Cronin et a1 , 1962; Haertel andOsterberg 1967) : 1) those associatedwith freshwater water masses, 2) thoseassociated with oceanic water masses, and3) those endemic to the estuary and associatedwith euryhal Sne waters, Neustonicorganisms, a1 though constf tutiny lesswe1 1 -established assemblages in estuariesas compared to freshwater or f~ord habitats,where turbulence and mixing are notas extreme, may include both distinctpopulations of zoopl ankters as we1 l asterrestrial dri f t organisms transportedinto the estuary.Freshwater zoop 1 ank ters transportedinto the upper reaches of estuaries canoften constitute a significant proportionof the estuary's zoopl ankton assemblage,especially in the 1 arge coastal estuarieswhere the riverine systems are largeenough to maintain stable zooplankton populationswithin the rlver itself. Thisis particularly true for the Columbia Riverestuary and Grays Harbor, where highdensities of the cladocerans Da hniaspp., Bosmina spy. , Ceriodayhnia -Y-s gua-+rangul a,~hanosoma brachyurum, them d copeyod Dia tomus spp., and thecyclopoid copepods yc opS spp., especiallyC. vernalis, are commonly found duringsumFer months {tlaerte'l and Osterberg 1967;Simenstad and ~~c.jers 19811. Haertel andOsterberg (1967) recorded the highest density( 2,700 rn-3) of freshwater zooplankters37 km from the mouth of the ColumbiaRiver estuary duri ny the period of maximumtemperature and lowest turbidityThe density there fell to below 100 m-3during the winter period of low temyeraturesand high turbid3tY. Densities ofpelagic zooplankton, i ncluding many fresh-water forms, in a riverine channel habitatof Grays Harbor reached maxima ofonly 30-60 rn-3 through the summer months(Simenstad and Egyers 1981).Oceanic zooplankton inundate estuariesvia the tidal intrusion of marinewater masses and become most prominentduring periods of lowest riverine di s-charge. Along the Pacific Northwest coastthe prominent marine zoopl ankters transportedinto coastal estuaries include thecl adocerans Evadne nordmanni and Podonspp., the cal anoid copepods Cal anus spp.,Pseudocal anus mi nutus, Cent ropayesabdominm Epilabidocera amphitrites,and Acartia spp., and the cyclopoidcopepodsyeaeus angl i cus and Oi thonasimilis; E ilabidocera is a neustonicform.Conslderab e seasonal variation indominant zoopl ankters transported intothe estuary occurs as a result of changesin nearshore currents and nearshore marinecommunity structure. Miller (1972)and Frolander et al, (1973) illustratedthat northern coastal or subarctic oceanspecies, such as the marine calanoid copepodsAcartia clausi and Pseudocalanussp., dominated theoopl ankton assembl ayeof Yaquina Bay in summer, reflectingsoutherly surface currents offshore, whileduring the winter neritic species characteristicof the California coastal assemblaqes such as Paracal anus --~arvus . Cteno--- calanus vanus, 'Clausoca ~anus arculcorni s,and the cmuoia ., rcoueood Corvcaeus - anul i-4 - -.- cus were transuortid' into the bay froinnorthward-f lowi ng nearshore currenis andbecame codominant with A. clausi.--Prevalent marine zoopl ankters inGrays Harbor also varied over the sprinyfallperiod as documented by Simenstadand Eggers (1981). ~vadne- nordmanni ,Podon sp., Pseudocalanus spp., Acart ialongiremis and A. tonsa were c o m m o ~duriny summer Throughmid-fa1 1 ; Calanussp. and Metridia lucens occurred yredomi nantly in late winter to early spring;and Centropages abdonlinal is and Acartia--clausi occurred abundantly from springthrouqh early surnmer. Densities of themarine zooplinkton assemblage in the ColumbiaRiver estuary appeared to peak at1.750 m-3 in the fall, with average

densities of % 500 throughout the year(~aertel and Osterberg 1967 ). Densitiesof neritic zooplankton at the entrance toGrays Harbor, which was dominated wholelyby marine euhal ine forms, reached an earlymaximum of %850 m-3 in April and a second,fa1 1 rnaxima of %200 m-3 but averaged~200 m-3 over the entire period. Meanstanding crop illustrated yreater fluctuations;estimates in the spring tell between200 my m-3 in April and 1 y m-3in early June but reached a maximum ofonly a10 mg m-3 in the fall. The averagemean standing crop over the entire periodwas 55 mg 111-3.Endemic zoopl ankton which sustainpopulations within Pacific Northwestestuarine channels are dominated by thecalanoid Eurytemora spp.; E. affini; predomi-. nates in the Columbia Hivertuarv(Haertel and Osterberg 1967; English 2al. 1980) while - E. americana appears toprevail in many of the other coastalestuaries such as Grays Harbor (Simenstadand Egyers 1981), Yaquina Bay (Frolanderet al. 1973), and the Salmon Riverestuary (Johnson 1981). Eurytemora tendsto completely dominate the zoopranktonassemblages in the mesohaline reyions ofthese estuaries and can attain high populationstanding stock levels under certainlow riverine discharge salinity regimes.Haertel and Osterberg (1967) reportedtwo peaks in Eurytemora density inthe Columbia River estuary, one in April(108 x 103 m-3) and another in July (39 xlo3 mm3). Eurytemora were most prevalentwhen surface salinities were 0.Z-8°/00,when the mean of the top and bottom salinitieswas 0.2-16°/00, and when the bottomnull zone minimized tidal flushing losssalinitywas greater than 0.2°/00. x- es. The abundance of adults was, howevtemorain Grays Harbor was second (20% of er, controlled by intense, size-selectivemean total density) only to Acartia cla~si predation by zooplanktivorous pelagic(22%) and also illustrated two denslty school iny fishes (see Section 9.1).maxima, one in late April (408 m-3) andanother from Auyust to the end of OctoberIn addition to normal sexual repro-('~80 m-3). In Yaquina Bay, Johnson duction of overwintering adults, replen-(1981) documented that, unlike ecartia i shment of endemic zoopl ankton populationsclausi which occurs seasonally ln the after low abundances during unfavorablewinter and Spring months may also be-reaches, the congeneric 6. califofniensiswas able to persist as an endemlcm i o n in the upper region of thatestuary.Maintenance of ende~ni c z00p1 anktonpopulations in Paci t ic Northwest estuarinecnannels can pose a major problem dueto the typically short flushing times,high deyree of turbulent mixing, and netseaward flow common at almost all depthsduriny the spring and summer. Unlike thei ndi yenous estuarine zooplankton popul a-tions in other regions, which haveevolved reproductive rates and verticalmiyration to compensate for the seaward1 oss of zoopl ankters , E urytemora popul a-tions in pacific Northwest coastal estuariesappear to be more vulnerable to depletionduriny high di scharge flushing.Possible a1 ternative rnecnani sms, such aslateral migration or entrainment in lowvelocity water masses such as in the nullzone or epibenthic boundary layer, mayexpl ain the persistence of Eurytemorapopul ations in these systems. Nevertheless,extreme riveri ne discharge andflooding have been reported to reduceEurytemora populations in the ColumbiaRiver by three orders of magnitude(Haertel and Osterberg 1967).A classic study of estuarine maintenancein a pelagic zooplankton populationis Johnson's (1981) revealing analysis ofAcartia californiensis in Yaquina Bay.m r s i s t e n t occurrence of we1 1-def inedcohorts in the upper region of the estuarywas concluded to result from short lifeexpectancy of adult females, with minorreinforcement from spri ny tides. Hssum-ing passive behavior, tidal flushing wasestimated to remove a rnaxirnum of 3.4% to8.7% per day, but actual behavioral utilizationof the landward flowing countercurrentand residence in the estuary'senhanced by the hatching of dormant orresting eyys which have overwintered inbottom sediments, as has been documented

for Acartia cal iforniensis in Yaquina t3ay acterization of pelagic zooplankton and(Johnson 1981).neuston commorl to estuarine habitats ofthe Pacific Northwest are presented inA yeneralized illustration and char- Fig. 5.4 and Table 5.4.CHANNEL SLOPESTONIC (DRIFT) INSECTSONlC CALANOIDWASPSEPU.bMQCara mphitr4ssMARINE COPEPODSP $ ~ ' minutus m .Evadne nordmMnrcolycwus mg*us Cm*, s(M0x)ronn rm*ls . L(,EAMEGALOPSFISH EGGS & LARVAEFig. 5.4. Representative ill ustration of common pelagic zooplankton and neuston assemblagesof estuarine channels of the Pacific Northwest.64

Table 5.4. Itemization and characteristics of pelagic zooplankton andneuston common to estuarine channel habitats of the Pacific Northwest.TaxaChannel~abi tats1Re1 evantSal i nity Life History~ssociations2 CharacteristicsCOELENTERATACordyl ophora sp.POLY CHAETAPol ynoi daeSpionidaeM E,P LarvaeME7PME, PLarvaeLarvaeGASTROPODAMytilus sp.VENEROIDAMacoma sp.MM7SM-BE-ME-ME-MLarvae and unsettledjuvenileLarvae and unsettledjuvenileLarvae and unsettledjuvenileROTIFERABrachi onus spp.Asp1 anchna spp.R-MR-MCLADOCERADaohnia SDD.Chydorus spp.Di aphanosoma brachyurumR-0R-0R-0E-ME-MR-0R-0R-0COPEPODACALANOIDACalanus spp.Paracal anus spp.Pseudocal anus mi nutusMetridia lucensCentropages abdominal i sDi aptornus spp.Eurytemora spp.Epi 1 abidocera amphi tri tesAcartia spp.E-ME-ME-ME-ME-0R-0R-EE-0E-M(continued)55

Table 5.4.Continued.TaxaHARPATCICOIDAChannel~abi tats1Re1 evantSal i nity Life History~ssoci at ions* CharacteristicsCYCLOPOIDAParacyclops fimbriatusOi t hona simi 1 i sBALANOMORPHA M- B Cypri s 1 arvaeMYSIDACEAAcanthomysi s spp.Neomysi s spp.CUMACEALeucon spp.CumelTa spp.MYSM-BE-MR-EAMPHI PODACorophi urn spp. R-E Pri nci pal 1 yadult males andEogammarus confervicol usM- Bjuveni lesPrincipallyadult males andAni sogammarus spp.juvenilesMYSJuvenilesISOPODAGnorimosphaeroma oregonensi sBOPY R I DAE M,S Juveni 1 esDECAPODACrangon spp. R-E PrincipallyCancer spp.PI NNOTHER IDAEUpogebia pugettensi sM-BE-ME-0E-MjuvenilesLarvaeLarvaeLarvae(continued)G6

TaxaTELEOSTE IEngraul is mordaxOSMERIDAEGAD I DAECottus asperGOB IDAEINSECTAEPHEMER ILLIDAEGERRIDAEPLECOPTERAPERLODIDAECHIRONOMIDAETab1 e 5.4.Concl uded.Re1 evantChannel Sal i ni ty Life History~abitatsl ~ssociations2'~haracteristicsM E-M Eggs and larvaeM E-0 Eggs and larvaeM E ,P LarvaeM-B R- E LarvaeM E-0 LarvaeM- B R-EM- B R-EM-BR-EM-BR- EM- B R-E Incl udi ng 1 arvaeARACHNIDAHYDRACARINA M- B R- E1~ = mainstem; S = subsidiary; B = blind.ZR = riverine; 0 = oligohaline; M = mesohaline; P = polyhaline;E = euhaline.

CHAPTER 6FISH ASSEMBLAGES OF ESTUARINE CHANNELSAccording to tnei r association withthe bottom or water column, fishes ofPaci fic Northwest estuarine channels canbe cateyori zed respectively as demersalor pelayic. In many instances, however,there is considerable overlap in speciesoccurrences in the two habitats due tobehavioral (vertical miyration, salinitypreterences) or 1 i fe hi story (demersal orpelayic larvae, spawning activity)characteristics.6.1 DEMEHSAL FISHESDespite the typical ly dynamic cnaracteristicsof the benthic environs of estuarinechannel habi tats, diverse assemblayesof derrlersal fish have become adaptedto live and reproduce amid the turbulentnixiny, high turbidities, low light levels,and variable food resources there.Unlike the salmonids , which have beenstudied extensively in many Paci tic Northwestestuaries, de~nersal fish assemblayeshave been relatively ignored. Only recentlyhave comprehensive research proyracrlssuch as the CREOOP studies on theColumbia River estuary and those fundedin Grays Harbor by the U.S. Army Corps ofEnyineers documented de~nersal fish assemblagesin channe Is throughout the estuaries,Synthesis of these sources (Natl.Mar. Fish. Serv. 1980, 1981; Simenstadand Eggers 1982; C. Simenstad and D.Ar~nstrony, School Fish., Univ. Wash..unpublished data) and more 1 imited informationfrom the Columbia River estuary(tlaertel and Osterberg 1967; Durkin 1975;Durkin et al. 1976, 1979, 1981; Higley eta1 . 1976), other coastal Oregon estuaries(Percy et al. 1974; Heimers and Baxter1976; blullen 19771, the Fraser River estuary(Northcote et al. 19791, the DuwarnishRiver estuary (lufatsuda et a]. 1968), andCommencement 8ay (We i tcamp and Schadt1981) indicate that 43 species (Table 6.1)of demersal fish occur commonly. Ufthese, nine species (denoted by *) generallyoccur in most estuaries (Fig. 6.1).Assembl aye structure varies si gni ficantlyamong these estuaries, however. Sourcesof this variation are myriad but appear torelate principally to the relative extentof salinity intrusion, the characteristicsof the freshwater watershed, yeoyraphi cregion, and estuarine microhabi tat.The effect of sal ini ty intrusion andflushing characteristics in structurinythe assemblage is most evident when thedecnersal fish assemblages of the Columbiaand Fraser River estuaries are co~npared tothose of less freshwater-dominated codstalestuaries 1 ike Coos and Yaquina Bays.Whereds euryhal ine taxa such as the coastalsurfperches (the hexagrarn~nidsspp.; lingcod,commonly inside the 1 atter bays, they seldomenter the Colu~nbia or Fraser Riverestuaries beyond the narrow euryhal i neregion within the first 2-3 km.The diversity of the demersal fishassemblage within a given estuary typicallyvaries as a function of the fishesisal i ni ty tolerances and habitat requirements.The National Marine Fisheries Ser-vice (1981) described the diversity (Shannon-WeaverIndex, H1 ) of bottom trawl -capturedfishes in the Columbia River estuaryas reaching a maximum mean value (H'; =2.4) between 9 and 23 km upstream from themouth of the estuary and declining rapidlywhen proceeding upstream to a minimum H'x= 0.8) at the riverine extreme of the estuary(Fig. 6.2a). This conforms closelyto the results of Haertel and Osterberg(1967), who indicated that the greatestnumber of species and abundances offishes occurred consistently within the

Table 6.1. Itemization and characteristics of demersal fishes common to estuarine channelsof the Pacific Northwest.--- ---.------------.-----TeT;i;vd%i -meTaxa Channel Salinity Sediment life history--- (cmnon -- name) -- --- --- ----- habitats1 - associat ions? associations3 characteristics'! -PETROMYZONTIDAE+ %a%;+L. lridentataT~acif ic laniprey)M- S R-E N PM-S H-E N PSUUAL lDAESqualus acanthias M E N F-€8TSp%ij-domiRAJ 1 DAERa a binoculataSi tj i S T T - fM E S-G 0-EBACIPENSERIOAEAci enser medi rostris H M-E N F-EBP- breen s t u F e rA. transmontanus H R-E SC-B F-EIT~hi te sturgeon)SALMON I DAEProsoem wil liamsoni H R-H N F-El3m n t a n ~ iZiTitXsTCYPRINIDAEC rinus car io*rci7+*M locheflus caurlnus7 k i U m -Rhinichthys falcatusKeojard-dace)Richardonius balteatus7ilZEG--STn?-ieS;r----M-SM-sM-SM- SR-N SC-S 0R-N SC-G F-El3F-EM0-EllCATUSTOMI DAECatostomus macrocheilusrime sucker)M-S R -H N F-El3(;AD I OAES-CF-EPSYNGNATHIDAES n nathus le torh nchus-hi-CENTRARCH IDAEPomoxis annularis-pIiicrappie)-M-ESC-G 0-EP; Particularlyassocfated wttheelgrass and macroal yaeF-EPF-EPPEHCIOAEPerca f lavescensTvTTTow perch)(continued)69

Tab1 e 6.1.Cont i nued.--RelevantTaxa Channel Salinity Sediment life history(cornon name habitats1 - associations2 associations3 characteristics4 -EMBIOTOCIDAEAmphisitichus rhodoterusmdtail surfperch)Embiotica lateralistStripedseaperchlS-C 0-EP; Particularly associatedwith eel grass,macroal gae, andstructuresM-B 0-E SC-B F-EP; Particularly associatedwith eel grass,macroal gae, andstructuresM-SP-E G-Cn F-EPMP-E N F-EPH. anale MTsootfin surf~erch 1ti 'elli ticumT i i h i r c h ) *P-E N F-EBP-E N F-EBST ICHAEIDAE*Lum enus sa ittt-*r&acx )PHOL IDAEPhol is ornata(Saddle~unne 1 )M-B 0-E SC-G F-MB; Common to eelgrassbedsS-B M-E S-G F-EP; Particularly associatedwith rnacroal yaeAMMOOYT IDAEHEXAGRAMMI DAEH. 1 agocephalusTROC~ green1 i ny)0 hiodon elonyatus?&ICOTT IDAE*Cottus aspert m l y sculpin)M-SM-SM-BM- BM-EM-EM-ER-MES-GSC-GS-C0-EP; Frequently buriesin sand; otherwisepelayicF-EB; Particularly associatedwith microal gae;Ipelagic larvae andearly juvenilesIF-EB; Particularly associatedwith mi croal yae;pelagic larvae andearly juveni les0-EB; Particularly asso- Iciated with microalgae;Ipelagic larvae andearly juvenilesF-EB*Le tocottus armatus7 h . a w c u l pi n)Scor aenichth s marmoratus7m:+,M-6MR-EP-ESC-CS-CAGNOIDAEStel lerina xyosterna M P-E S-C F-EB(Pri cklebreast poacher)CYCLOPTER~OAEM- S M-E S-C F-EP(con ti nued)70

Table 6.1. Concluded.- - -. .- - .--- *-- '----. -- - -- .- - -RTeeVnt-' - ---Ta xa Channel Salinity Sed i mnt 1 ife history(comnon name) - ------- - habitats1 __--associatio_n~~ asso~iati~~s~s~~5hara~teristi~s4 --L. rutteri M-S P-E S-C F-EPTRi-snai1 fish)Citharichth s sordidusd d ~ .*Fipstiy;euseck e sanddab)M- S M-E S-C F-EP; Pelagic larvaeM-SM-EF-EP; Pelagic larvaePLEURONECTIDAEM-SS-CF-EB; Pelayic larvaePLEURONECTIDAE - continued*Par0 hr s vetulusM-Bv * s rM-E SC -C F-EP; Pel agl c 1 arvae*Platichth s stellatus M-B H-E SC-C F-EB; Pelagic larvaeT s G i + k u rPsettichthys melanostictus M-S M-E S-C F-EB; Pelagic larvaeIsand sole)*species prevalent in all Pacific Northwest estuarine channels.= mainstem; S = subsidiary; B = blind2~ = riverine; O = oligohaline; M - mesohaline; P = polyhaline; E = euhaline~ S C = siltlclay; S = sand; G = yravel; C cobble; B - boulder; Cn = consolidated; N nodefinitive sediment association.4~ = parasitic on other fish; F- facultative, 0- = obligate; PP a pelagic planktfvore; EP =epibenthic planktivore; EB = epibenthic benthivore; MB = meiobenthic benthivore; 0 8 omnfvore.oligohaline to mesohaline regions nomatter where this mixing region waslocated within the estuary due to variabilityin river discharge. Durkin et al.(1981) also indicated that abundance ofdemersal fish was hiyhest in those channel("scour") sites witnin the mixing ornull zone region of the estuary, whilediversity decl ined uniformly as distancefrom the mouth of the estuary increased.The compounded effects of fish emigration,immi yration, and recruitment ofjuveniles, and of river discharge onsalinity distribution within the estuaryalso account for seasonal shifts indiversity of demersal fish assembl ayes.From the same 18-month, 22-site bottomtrawl sampling series cited above, theNational Marine Fi sheries Service (1:81)also documented that peak diversity (H, =2.2) occurred between October , ahdDecember, and mininium diversity (H; =1.2) occurred between May and July (Fig.6.2b). The occurrence and extent of thedensity minimum may, however, be unrepresentativebecause of the unusual effectsof the drarnatical ly-increased turbiditylevels during this period as a result ofthe May 18, 1980 eruption of Mt, St.Helens in the Columbia River watershed.Among the principal demersal fishes inthe estuary, starry flounder, pricklysculpin, and Pacific staghorn sculpini 1 lustrated tew major changes in nurnericalavailability over the 18-month period;availabilities of shiner perch, Pacificsand lance Enylish sole, and buttersole, on the other hand, fluctuated bothmonthly and seasonal ly ; snake prick1 e-back, sand sole, and Pacific tomcodavailability varied intermediately on aseasonal scale.6.2 PELAGIC FISHESUnl i ke demersa I tish assemb 1 ages,pel ayic fishes in estuarine channelhabitats otten occur sporadically because

Fig. 6.1. Representative illustration of common fish assemblages of estuarineof the Paci f ic Northwest.channels-:x 2 .r,*$aW>8 1.-:X 2.I>5 -WZ0 1..10 10 20 30 40 50 60 FEE MAR AQR MAY JUNE JULY hUC SEPT CCT NOV M C JAN FEB MARMSTANCE FROM MOUTH OF ESTUARY (km) 19001981DATEFig, 6,2. Mean Shannon-Weaver diversity index (HIK) of demersal fishes in the ColumbiaRiver estuary as a function of location along the longitudinal axis of the estuary (A)and aver the 18-month sampling period (B) ; figure from Natl. Mar. Fish. Serv. (1981).7 2

of their motility and characteristic associationwith discrete water masses or asa function of life history patterns. Forinstance, the occurrence and residencetime in the estuary of anadromous speciesis general ly a function of miyratorybehavior. Many species occur solely aspelagic 1 arvae and juveni 1 es (meropl ankton)during brief periods in their earlylife history but emigrate from the estuary,become demersal , or move into adjacenthabitats as juveniles and adults.Similar to the information aboutdemersal fish, the majority of the comprehensivestudies of pel agic fish assemblayesin estuarine channels of the regionhave occurred in the larger estuariessuch as the Columbia River (Haertel andOsterberg 1967; Durkin et al. 1979, 1981;National Marine Fisheries Service 1980,1981), Grays Harbor (Simenstad and Eggers1981), and the Fraser River (Northcote eta1 . 1979) ; some small er, coastal estuarieshave been surveyed, however, i ncl udingCoos Bay (Cummings and Schwartz 1971),Ti 1 lamook Bay (Cummings and Berry 1974;Forsberg et al. 1975), the Umpqua River(Mullen 1977), and Sixes River (Keimersand Baxter 1976). Ichthyopl ankton hasalso been addressed specifically in theColumbia River estuary (Mi si tan0 1977;English 1980), Yaquina Bay (Pearcy andMyers 1974), and Humbol t Bay (Eldridgeand Bryan 1972) and incidentally in GraysHarbor (Simenstad and Eggers 1981). Synthesisof these sources indicates that 36taxa representing 16 families are commonfishes in the pelagic assemblages of Pacific Northwest estuaries (Table 6.2).Of these, 13 are anadromous, 16 appearexclusively as ichthyoplankton, and onlythe remaining eight comprise taxa whichcould be considered to maintain extendedresidence in estuarine channel s.Unlike the pattern of demersal fishassembl aye diversity in the ColumbiaKiver estuary, the National Marine FisheriesServise (1981) documented maximumdiversity (HT = 1.7) of pelagic (purseseine-cauyht) fishes in the central mixingregion of the estuary, 20 to 35 km fromthe mouth, and below average diversityvalues in both euryhaline and riverineregions (Fig. 6.3a). Temporal diversityof the pelagic fish assemblage was alsodramatically different from the demersalassemblage. In an almost mirror image ofthe pattern of the demersal, fish assemblage,maximum diversity (Hz = 2.2) ofpelagic fishes occurred in tne, spriny anddeclined to a winter minimum (ti- = 0.5) inan almost mirror image of theXpattern ofthe demersal fish assemblage (Fig. 6.3b).As noted earlier, however, the effects ofincreased turbidity from the eruption ofMt. St. Helens in May 1980 may biasinterpretations of the May-July 1980data.6.2.1 Resident Pelagic FishesAmong the common pelagic fishes inestuarine channels, the clupeids (herrings),enyraul ids (anchovies), osmerids(smelts), atherinids (silversides), andammodytids (sand 1 ances), commonly referredto as a group as "baitfish," comprise the majority of the non-anadromous,resident fishes; the three-spine stick1 e-back comprises the only non-baitfish resident.Pacific herring utilize PacificNorthwest estuaries for spawning and rearingof larvae and early juvenile stages.Spawning typical ly occurs in shall ow subtidalhabitats between January and July,with considerable variation among estuaries.Spawning in the Columbia Riverestuary occurs between March and July andmay i nvol ve several major spawni ngs (Mis i-tan0 1977; Natl. Mar. Fish. Serv. 1981).In Yaquina Bay herring spawn earlier,between January and March (Pearcy andMyers 1974), and may a1 so undergo as manyas four major spawnings (Steinfel d 1972).Accordingly , 1 arvae may occur in thechannels over a protracted period oftime, between March and August in theColumbia River estuary (Mi si tan0 1977)and between January and May in YaquinaBay (Pearcy and Myers 1974). Spawninymay be annually sporadic, however, asboth English (1980) and Simenstad andEggers (1981) reported low abundances orno herring larvae in the Columbia Riverestuary and Grays Harbor, respectively,in 1980. Juvenile herring, whether originatingwithin or transported into theestuary as larvae or post-larvae, tend to

Tab1 e 6.2 I temi ration and characteris tics of pelagic fishes comnon to estuarine channelsof the Pacific Northwest.----.--- -Channel Salinity Re1 evant 1 i fe- Taxa-- habitats1 associations2 hi story characteristics3CLUPE IDAEAlosa sa idissima~ i *ENGHAULIDAESALMONIDHEOncorh nchus gorbuscha-Fix-hG)0. keta (chum salmon)U. kisutch (coho salmon)g. 'ner'kasockeye salmon)0 tsfiaw tscha76 h b n 1Salmo clarkiTcutth-rou t )S.t9a; rdneriee head trout)Sal vel inus malma'(Do1 ly Varden)0-E 0-PP; Anadromous0-E 0-PP; Also occurs in ichthyoplankton;spawn in estuaryM M-E 0-PP; Occur principally aslarvae and juvenilesM-B K-E F-PP; AnadromousM-BM-BM-SM-SR-ER -ER-ER -E0-EP ; AnadromousF-EP; Anadromous0-PP; AnadrornousF-EP; AnadromousM-B R-E F-PPs ; AnadromousM-B K-E F-PP; AnadromousM-S H-E F-PPs; AnadromousOSMEH I DAEH omesus retiosusfhlh-,S irinchus thaleichth sMM-SM-SM-SM-EM-E0-E0-E0-PP; Also occurs in ichthyoplanktonF-PP; Also occurs in ichthyoplanktonF-EP; Anadromous ; a1 sooccurs in ichthyoplanktonC-PP; Anadromous ; a1 sooccurs in ichthyoplznktonMicro adus roximusM-E 0-EP; Occurs only in ichthy--mktok oplankton; demersal as juvenileand adultATHER INIUAEAtnerinoys affinis M-S 0-E0-PP; Anadromous~asterosteus aculeatusnhree-spined stick1 eback)M-BR-E0-EP(continued)74

Table 6.2. Continued.- ---Channel Sal i nityRe1 evant 1 4Taxa -. habi tats1 associations2 hi story characteri stics3 -fkPERCICHTHYIDAEMorone saxatilis- m p mM R-E F-EP; AnadrofnousSTICHAEIDAE\urnpenus sagittaSnake prick1 eback)PHOC I DAEPhol is ornataw e m u n n e l )AMMODYTIDAEArnmod tes hexa terus-&s*M-S M-E 0-PP; Occurs only in ichthyo2lankton;moves to demersalhabitats as juveniles andadultsM-EM-E0-PP- Occurs only in ichthyoplenkton;moves to demersalhabitats as juveni 1 es andadults0-PP; Also occurs in ichthyoplanktonGOBI IDAEClevelandia ios(Arrow goby)-SCORPAENI DAESebastes melano sm o dSebastes spp.- ( = h )M-SM-EM-EP-EM-E0-PP; Occurs only in ichtiiyoplankton;moves to shallow1 ittoral habitats as juvenilesand adults0-PP; Occurs only in ichthyoplanktmmoves to shallowlittorsl habitats as juvenilesand adultsF-PP; Also occurs in ichthyoplankton0-PP; Occurs only in ichthyoplanktonHEXAGRAMMI DAEHexa rammos spp.*)0 hiondon elongatus-hM-EM-E0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadult0-PP.. Occurs only in ichthyoplankton;moves to demersalhabitats as juveni 1 e andadultC OTT I DAECottus asperv - l y scul pi n)M-BB-P0-PP; Occurs only in jchthyoplankton;moves to demersalhabitats as junen i 1 e andadult(continued)7 5

--- Channel Sal inity ~ eeiant l 1 i feTaxa habitats1 associations2 hi story characteri stics3Tab1 e 6.2.Concl uded.Le tocottus arrnatus.ldkiEXighorn scul p~ n)Scor aenichth s marmoratus7-PLE URONECT I DAElso setta isole is-&o+Paro hr s vetulusn+srPlatichth s stel latus1 4 u rPsettichth s me1 anostictus7-e-M-tcMM-EM-E0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadult0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadult0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadultM M-E 0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadultM M-E 0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andM 0 -Eadult0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile andadultM M-E 0-PP; Occurs only in ichthyoplankton;moves to demersalhabitats as juvenile and- -adult1~ ,. mainstem; S = subsidiary; B = blind211 rlverlne; 0 = oligohaline; M mesohaline; P polyhaline; E = euhaline30- obligate; F- = facultative; PP = pelagic planktivore; EP = epibenthicplanktivore; PPs = pelaylc piscivorerear in estuarine waters usually b 2UQ/,,sal fni ty through summer and late fa1 1. Atleast among the coastal estuaries, fewjuvenile herring contlnue to reside longerthan 8-10 months. Although Pacificherrf ny have been reported in inlandestuaries (Fraser River, Northcote et a1 .1979; Squamish River, Levy and Levings1978; Duwamish River, Matsuda et al.1968), most herring spawning and rearingappears to occur in the adjacent bays andfjords of Puget Sound and the Straits ofG@orgia and Juan de Fuca (Miller et al.1978, 1980; Miller and Borton 1980;Trumble et al. 1977; Meyer and Adair1978; Fresh 1979; Fresh et al. 1979;Gonyea et al. 1982). Herring spawningappears to be highly correlated with theoccurrence of substrates suitable for eggdeposition, such as eelgrass and macroalgae,and with moderately high water flushingrates. This may explain why herringspawning tends to be more pronounced insuch coastal estuaries as Yayuina Bay andCoos Bay than in more freshwater-dominatedestuaries such as the Columbia River estu-

1 , , , , , , , , I , , , , , . . , . . , , ,, . i0 10 2 0 30 40 50 . 60 FEE MAR IPR MAY JUNE JULY LI.#Q SEPT OCT NOV MC JAN FE8 MARDISTANCE FROM MOUTH OF ESTUARY (km)1680 1981DATEFig. 6.3. Mean Shannon-Weaver diversity index ( H I x ) of pelagic fishes in the ColumbiaRiver estuary as a function of location along the longitudinal axis of the estuary (A)and over the 18-month samplina period (B) ; figure from Natl . Mar. Fish. Serv. (1991!.ary, which has no extensive eelyrass orkelp bed habitats. Keariny of larvae andjuveniles in channels appears initiallyto be a function of offshore-estuarinecirculation and later, with their recruitmentfrom the plankton to the nekton, afunction of prey (cal anoid copepods, i .e.Acartia clausii , Pseudocalanus sp.)availabi 1 i t n s s e l l 1964; Pearcy andMyers 1974).Most northern anchovy eggs, larvae,and juveniles which occur in the region'sestuarine channels oriyi nate from spawningpopulations in adjacent coastal waters,although spawning has been reportedin bays and passages of Puget Sound (Mil l-er and Borton 1980). Kichardson (1973)described concentrations of anchovy larvaein near-surface strata of the ColumbiaKiver plume between June and August andsuggested that a spawning stock of anchovieswas particularly associated with theplume. Eggs appear to be commonly transportedinto the Columbia River estuarybetween Apri 1 and September. English(1980) described maximum densities (-1500m-2) in June at locations nearest themouth of the estuary. Hatching of theseeggs within the estuary and further transportof larvae into the estuary accountfor increased concentrations of 1 arvaeand post-larvae in the euhaline to meso-ha1 ine regions over an extended period,January through November ( Mi si tan0 1977).Pearcy and Myers (1974) also collectedlarval anchovies (1.6 x 10-3 m-3) fromYaquina Bay in July through Septemberalthough densities were not as high asreported in the Columbia River estuary.Probably due to a general 1 ack of signifi-cant sampl ing effort for small , school ingpelagic fishes in these estuaries, juveni1 e northern anchovy between post-larvaland the 2+-year age classes have not beenreported extensively. There i s qua1 i tativeevidence, however, that they are commonwithin estuaries (T. J. Durkin, NMFS,Harnmond, OR; pers. conirn. ) - Age 2+ andlater aye classes can be sampled bypurse seines and are reported to occurabundantly in the lower reaches of theColumbia Kiver estuary through much ofthe year (Nat. Mar. Fish. Serv. 1980,1981; Durkin et ale 1981 ) - Simenstad andEggers (1981) estimated that adult anchoviesmaintained residence in Grays Harborfor up to 6 weeks during two ~~eriods,mid-~une to early August and late ~ugustto early October, and resided longest inthe region just inside the mouth of theestuary. Juvenile anchovy, on the otherhand, sustained residence for a long as11 weeks, during mid-July to earlyOctober, in the mixing zone further upthe estuary.

Whitebait and surf smelts comprisethe non-anadromous osmerids which utilizethe region's estuaries. While spawninghas not been reported in coastal estuaries,surf smelt spawn on polyhalinebeaches of Puget Sound and the Straits ofGeorgia and Juan de Fuca (Hi 1 ler and Borton1980) and may spawn within the lowerreaches of some of the more marine-infl u-enced coastal estuaries (Quill ayute Riverestuary, Chi twood 1981). Whitebait smeltare rare inside the Strait of Juan deFuca, which is at the northern limit oftheir geographic range (Hart 1973), andlittle is known about their spawningbehavior other than that they are presumedto spawn in coastal waters (Hart1973). Osmerid eggs are common throughmuch of the Columbia River estuary duringApril and May (English 1980) and thelarvae are probably present untll January(Mi si tan0 1977) ; they were not reported,however, during Pearcy and Myers ' (1974)extensive survey of Yaquina Bay ichthyoplankton.Both s~nel ts are present asjuveniles in the Columbia River estuarythrough most of the year and have beenreported in relatively hi yh densitiesduring several months, i.e., June-July inthe case of surf smelt and July-Augustfor the whitebait smelt (Natl. Mar. Fish.Serv. 1981).Topsmelt is the least comnion ofthese nonanadronious pel agic fishes andoccurs exclusively in coastal estuariessouth of the Columbia River where spawningpopulations are reported in Coos Bay(Schultz 1933) and the Umpqua River estuary(Mullen 1977) between late May to earlyJuly. In both estuaries topsmelt capturecontinued in the upper reaches oftne estuary from late August throuyh Septemberand may have included as many asthree age classes (if 0-age class fishare presumed to remain within the estuaryafter hatching) residing in the estuary(Schul tz 1933).Pacific sand lance are a schooling,pelagic fish which is often associatedwith the bottom in sandy habitats (seeSection 6.1) where they periodically burythemselves (Hart 1973), a behavior relatedto photoperiod, food availability, andhunger (Kuhlman and Karst 1967; W i nslade1974a, b, c). Their attenuated body formand rapid swimming speed makes them oneof the hardest species to capture, muchless quantitatively assess their standingstock, and it is questionable that theirutilization of Pacific Northwest estuarieshas been documented adequately. Larvaehas been reported in euhaline-polyhalineregions of the Columbia Riverestuary in March-April (Mi si tan0 1977)and in Yaquin Ba in moderate densities(3.5 x 10-3 m ) from January throughMarch (Pearcy and Nyers 1974). The latterstudy illustrated that sand lancelarvae were more abundant offshore andprobably were transported into the estuaryvia tidal exchange. In the case oftne Columbia River estuary, sand lancewere captured throughout the year andwere periodical ly abundant (Nat. Mar.Fish. Serv. 1981). Larval sand lancehave been collected in the mesohalineregion of Grays Harbor, and common, abundantoccurrences of juveniles have occurredin polyhaline regions of the outerestuary (Simenstad and Eggers 1981).Threespi ne sticklebacks are ubiqui -tous fish which have been reported from avariety of freshwater and marine habitats(Hart 1973; Wydoski and Whitney 1979).They inhabit a variety of estuarine habitatsand are common in the surface watersof blind, subsidiary, and mainstem channelsbut are also found among littoralmacrophytes. Reproduction occurs in bothfreshwater and marine habitats (Hart1973), although Vrat (1949) has questionedthe effectiveness of reproduction in salineenvironments, Most of the comprehensivestudies in the reyion's estuariesillustrate consistent occurrences, abundances,and spatial distributions throughoutmost of the year (Mullen 1977; Northcoteet al. 1979; Natl. Mar. Fish. Serv.1980, 1981; Simenstad and Eyyers 1981),althougn a few, typically those of inlandestuaries, report fewer and less consistentoccurrences (Matsuda et al. 1968;Levy and Levinys 1978).6.2.2 Anadramous Pelagic FishesAmong the anadromouspelagic fishes78

utilizing estuarine channels, over halfare salmonids (Table 6.2). Because oftheir commercial and recreational importance,Pacific salmon and anadromous trouthave long been the focus of intensivestudies in estuaries throughout the regionboth as juveniles migrating from freshwaterto rear in inarine habitats and asadults returning to spawning rivers. Althoughthere i s no comprehensive synthesi sof this mass of knowledge, Iwamoto andSalo (in prep.), Ourkin (1982), Healey(1982), Myers and Horton (1982), andSimenstad et a1 . (1982b) have includedmuch of the existing information on estuarineutilization by salmon and furtherreferences can be secured from Levy(1980b) and Columbia River Estuary DataDevelopment Progra~rt (1980). Wh i 1 e therehas been no coinparable syntheses of theecology of anadromous trouts in this region,Royal (1972) provides the most comprehensivediscussion to date.Anadromous trouts--cutthroat, steel -head, and Do1 ly Varden--are comparativelyless abundant than the salmon and appearto utilize estuarine habitats sparingly;estuarine channels act principally ascorridors for their seasonal migrationsbetwen freshwater spawning habitats andmarine feeding habitats. After 2 to 9years (typically 3 years) in freshwater,coastal cutthroat initially immigrate toestuarine and marine habitats during thespring and reside there until late summerand fall (Wydoski and Whitney 1479). Ofall the trouts, cutthroat trout and DollyVarden may utilize estuarine channels themost, since throughout their marine periodthey appear to stay in the vicinity oftheir home streams and often reside permanentlywithin estuaries (Levy and Levings1978). A1 thouyh sustained estuarine residencehas seldom been illustrated, ljiger(1972) indicated that pre-smolt cutthroat(up to 170 mm FL~) which moved into theAlsea River estuary in the later part ofthe spring emigration maintained nonmigratoryresidence within the estuary.Both steel head and Do1 ly Varden immigratethrough the estuary from freshwater to4~~ = Fork length.the ocean in late winter and spring, althouyhthe racial population structure ofsteelhead is such that some juvenilesteelhead may be found migrating to seaduring every nlonth of the year (Wydoskiand Whi tney 1979). Similarly, whileDolly Varden appear to be liini ted to sub-sequent emigration back into freshwaterin late summer though early fall, miyratingsteelhead may pass through the estuariesthroughout the year. The principalperiods when adult steelhead ascend spawningstreams is from December to March(termed "winter run1' fish) or betweenJuly and September (I1sumrner run")(Wydoski and Whi tney).The occurrence and extent of utilizationof estuarine channel habitats byfive species of Pacific salmon are highlyvariable because of their diverse lifehistory patterns (Table 6.3). Extendedoccupation of estuaries beyond the normaltime required for direct migration to andfrom the ocean is suggested to benefitsalmon by providiny an environment forproductive foraging, physiological transi-tion, and refuyia from predators (Simenstadet al. 1982b). Estuarine residence,the habitats occupied, and the total residencetime of outmigrating juveniles aredetermined primarily by the timing of andsize at entry into the estuary. These,in turn, are correspondingly influencedby numerous abiotic and biotic factorsoperating in the freshwater system, i.e.,time of adult spawning, stream temperaturesduring and after egg incubation,fry size and condition, population densityin the strearn, food quality and quantity,stream discharge and turbidity,physiological change, tidal cycles, andphotoperiod (Iwarnoto and Salo, in prep. ).Juvenile pink and chum salmon typically enter the estuaries at 30-40 mm FL,and occupy littoral and shallow suh-1 i ttoral habitats in the estuary. Whenthey are 45-55 mm FL, they begin occupyingthe pelagic surface of channels untilthey leave the estuary. Similarly, subyear1ing (often referred to as "fry")chinook salmon which enter the estuary30-50 mm FL in size also tend to occupy

Table 5.3. Life history characteristics of five species of Pacific salmon in northeasternPacific Ocean region (modified from Simenstad, in press).WdzsmrySat wn Spec i CIWare Pink C*n hho--- Qcteye Chinmi.%amins ioc~t%on km ?n wall trtbutaries SQat In malt triautdrler Pttadriiy in swll rivers PribUtdries f5 Ibkes. in trlb~t6rles. mstand Timingand e~t~arjne intertida:, amt estuarine rwemidat. am trfbutss>es t n sloe ~ ~ s &iony r lare shore- in win rivers. occurs overmbt ln large CrlDUtdrl65doff =in rivers; occursost ln Jars crtaitarles mannels of Larye rivers,am niin rlvers. ~ccurs =Curs over one to tatine, occurs over ta tofarr mntns fros lateone to tro mntns in fallexcept tor .spri% cnrnook-~ v e r o l q ~ o t w ~ orermemtnfr[*edrl~ ~ s r np~tfrsfromlatefall s~rertoldtefdll populatrons, wnicn spawnedrly fdl t. pti~rlly OQd fa! 1 throvyn earl1 dnter tnrqn early winter over three to SIX mntn5 lnyeam in ~aclflc northwestand Sovthearsernsprlny thruuyn early fall.snll s&aner runs occur inLIIsLI, even yearr Puet sound and the ColuslelsahereI* hid~kabia River and a wlnter runoccurs In tne SacrarrntoRiver%rat ton of EygOevelopentI ~ ~ i of n g FrrEmergenceFresnwater RedringTimIny and DurationOuration and Timlngof Cnlgrdtton toEstuaryDuration andLOC~~~MI ofResidence lnEstuary andNearsnore MarineEnvl ronar?ntPreferred PreyOradnlsms InM%yration andResidence In HorthPacificfnree to t3ve nsntnsBid- to late ulnterUsually aigrate~tseoiately afterenergenceOccurs over one wnfnbetween rid-winter toearly sprinyLess tnan one wtek inshallm habitats. threeto five weeks in neritlcndot tatsCalanoia copeyoas. andlarvacedns In neritlcAlong cwst in wlf ofAlaska, Easterr, BeringSea dnd Aleutian lslandsfor approxiniltely OMyearTnree to I1 we mtnr la to fln wtbs Three to five mnths Tnree ro five mtnsma- to 1dLe nnter.early spring(nd-wlnterEarly to late winter0 ~ ~ 6 slyrate 1 1 ~Thrwyhwt the year. Tnrou* one to tnreeil*.edtately afzermergence. one -nth12-28 months In stream.as lonq as three yearsyears in lakeurlmin AlaskaOccur5 over one rantn Uccurs orw one to four Utcurs over one to t*om+*(ten rld-rSntcr ma motns In lste winter to wncns In early r5 latelate spring earl] :ur S P ~ ~ Wb e to tnrep weeks in Un to hm mntns rn Short-tern, one to t4snallw ndbitdts, three neritfc nabttats: sols weeks in nericic nabitatsto live pets in nerittc ertendRd rearing, up tohaottlts; SDle extended SIR mntns. in inlandrearing. up to six seasuontn5. in 1nlrM searHdrpa~tl~~id copepods and -rid ampnlpods in Juvenile snrinp aodrid ~ hlyods in shaltor s~bllttordl wuha~slias in nerltlcinal lor sui~itloral nab~tass; decapod larvae nabitatshabitats; ~dldII0id and wpnaustids Incooe~as, deca~~d larvae. neritic nabitatsand iarvaceans' in neritichabitats&long coast in Gulf of Alony coast in Gulf ot Alooy coast and in GulfAlaska, Eastern Bering Alaska and Eastern of Alaska for t*it toSea and Aleutian Islands Aleutian Island for one, tnree years except forfor tnree to flve years usually two years western Alaska@puIations, which alsomature in &ring Sea andAleutian IslandsTiming of Return Late sumr to early fall Edrly fall to early Late sufmner to mid-fall Hld-sumr to early fallMiyratlon towinterEstuarylNatalSt ream -me-winter to lace sprinyexcept for 'spriny chinook"populations, wnich emergefraa fall thrwg mfdwtnterSprsny through suumer,tnree to fwr mnths $0stream, except for "sprlnychiwok' populdtians, wnichtend to rear for full yearin estuaryOccurs over one to twomntns from &a-minter tolate suner except for'spriny chinookm @pulatrons.wnicn emgrate fraafell rnroup winterb e to tnree weeks insnallw habitats, tn, tosix weeks in neriticnab1 tats. some extendedrearlny. elynt to ten reeksor lonyer. In ldryeestuaries and inland seasbaamaria anylnipods,cumceans, and emeryent andorirt insects in shallowsubl~ttoral nabitats; driftinsects, deCaood larvde andfish larvae in neritichdbitdtSAlony codst in bult otAlaska, Eastern Bering Seaand AleUtldII ISldnds torone to flve. typicallytnree yearsFdll except for "sprlnychinook" ~opulations, wnicnreturn in mid-spr(nytnrougn earl> fall ---

1 i ttoral and shal low sub1 i ttoral habitats,particularly sal t marshes, mudflats, and foreshore areas before theygrow larger and move into the pelagicenvirons (Levy and Northcote 1981; Congletonet a1 . 1982). Little is known aboutthe distribution of chinook (fry) duringflood tide cycles when sal tmarsh and mudflathabitats are inundated. It is oftenpresumed that they move about and feedover the littoral flats. Healey (1980),however, captured no juveni le chinook(fry) in this habitat of the NanaimoRiver estuary during purse seinesampling at flood tide and the fish werefound across the landward margin of theflats along the edge of the saltmarsh. Asimilar distributional pattern was alsodocumented for juvenile chum in the NanaimoRiver estuary (Healey 1979). But thefish are at least periodically congreyatedin the blind and subsidiary channelswhich transect most littoral and shallowsublittoral flat habitats during ebb tidecycles, and it is here that most biologicalsampling has been concentrated (Fig.6.4). Finger1 in'g and year1 ing chinookand coho smol ts emi grate directly intothe pelagic habitats of estuarine channelsand, except for occasional foraysinto shal low sub1 i ttoral nabi tats, residewithin this habitat until they depart theestuary.Almost a1 1 juvenile salmon migrateinto estuarine habitats between mid-winterto late summer, with some Speciesi 1 lustrating concentrated migration periods(pink, chum, sockeye) and others(coho, chinook) protracted migrations asa result of variable population (racial)and environmental factors. Table 6.4( Simenstad et al. 1982b) summarizesdocumented species residence times (totaltime juvenile salmon of particular speciesoccur in estuarine habitats) for WashingtonState estuaries, and illustrates thatjuvenile pinks may occur in some estuariesover as little as four weeks whilejuvenile chinook may occur over as longas 29+ weeks. In estuaries adjacent toPuget Sound and the Straits of Georgiaand Juan de Fuca, where resident chinook("blackmouth") and coho salmon populationsare sustained, juvenile and imature chi-nook and coho may continue to frequenteuhal ine seglnents of estuarine channel ssporadical ly throughout the Year (Simenstadet a1 . 1982b).Species residence times, however, reflectboth the variable turnover in transitionalmigrants from a diverse spectraof stocks and variable ~eriods of SUStainedresidence of each cohort groupwithin the estuary. unfortunately, theextensive and expensive method01 ogy haslimited the number of re1 iable estimatesof individual residence times and identificationof the factors regulating estuarineresidence. Simenstad et a1 . (1982b)have 1 isted estimates of maximum residencetime for cnum, coho, and chinook salmon,including several specific to estuarinechannel habitats, in Washi ngt0n estuaries(Table 6.4). Both juvenile chum and chinook(fry) appear to have short residencetimes in saltmarsh tidal channels, on theorder of tour and six days, respectively(Conyelton et al. 1982). This is furthersupported by Levy and Northcote's (1981)approximation of 6 days individual resi -dence time of juvenile chinook in aFraser Hi ver estuary bl i nd tidal channel.However, because nos t of these sal t-narsh/mudflat tidal channel studiesexamined residence in only one channelsystem and because occupation of aspecific channel may be brief, overallresidence throughout the bl i nd and subsidiarychannels of sal marshes and tideflats may be significantly longer. Levyand Northcote (1982) indicated maximumindividual residence times of 30 days forjuvenile chinook (fry), 11 days for chum,and two days for pink. Levy et al.(1979) had also indicated that juvenilechinook (fry) had the Strongest fidel ityto particular tidal channel areas,followed by juvenile chums, and juvenilepinks. They suggested shortest residencyfor juvenile pink salmon, intermediateresidency for juvenile chum, and longestresidency for chinook (fry); the variationin residency was possibly related totheir distribution within the channels andthe timing of emigration on ebbing tides.Detailed mu1 tivariate analyses of spatialdifferences in tidal channel uti l izationby juvenile salmonids in Fraser River

Fig. 6.4. Tidal channel trap net set in blind channel of Fraser Rivar estuary to samplejuvenile salmon utilizing saltlnarsh habitat; net is set at flood slack (A), allowed tosarrrple thr-ough the ebb tide (R, C) , and sarllpl ing culrllinated at ebb slack (0) when only asnrall depth of water remains in the channel (photographs courtesy of David Levy. NestwaterResearch Centre, University of British Colurnhia, Canada).saltnrarshes has also indicated that juverillech~nook (fry) abundance IS highlycorrelated to the amount of habitat ava~lableto the frsh, Lower (bank) elevat~onareas tend to support higher dens'ities ofjuvenile chinook (fry) (Levy and Northcow1981). Variables included tidalchannel descriptors such as inouth wldth,station width, channel length, channelorder, sub-channel length, mean angle ofcnannel bank, tidal slope, high tideheight. tidal channel area, bank elevation,area of subtidal refugia, and numberof hours of tidal channel subrnergenceprior to sampling; (see Appendix 6).Following residence and growth inthe littoral flat channels, juvenile chumand chinook (fry) move into larger subsidiary and mai nstern channels (Heal ey 1979,1980; Simenstad and Eggers 1981). Thistransition from 1 i t toral and shall ow sub-

Table 6.4. Species residence times (weeks)' of juvenile salmon in !lashinaton Statcestuaries; niaxiiliuni individual residznce times (days) are indicated in parentheszs (froniSiinenstad et a1 . 1982b).-- .-- ----- . .- -----.-- -- ---.--- EstuaryP iii -----CXUmum-Sock ey e. CKook-. -.-.- .-- - Source- - - --- - ---- - -.- . ---- ---Northern Puget Sound (nearshore) 4 6 12 12 6 Miller et al. 1978North Sound (Bellingham Bay) 11+ 114(Bellingham Bay) 7+ 7( nearshore) 4 6 6Skagit BaylPort Susan (Kiket Island) 13 13 12(saI tmarsh) 14+, (4)Elliott Bay (lower Duwamish)(estuary)(lower Duwami sh)Cornencement Bay (estuary) 16+ B 9(Hylehos Waterway) 9ll+ Tyler 19646+, (-20) Sjolseth 196R6 Miller et al. 1978;Fresh 191915, (50) Stober et al. 1973b16+, (6) Longleton et dl. 19G28. (42) Bostick 19558 Salo 136916+ Mcyer et al. 1981b9+ Puyallup lndian Nation,unp11bl.8+ Meyer et dl. 198laNisqually Reach 12 17+ 15, (-40) 11+ Fresh et dl. 1979Hood Canal 18 23, (32) 15, (6) 13 Salo et al. 1900Strait of Juan de Fuca 14 14 14 16+ Slmenstad, unpuhl.Quil layute River estuary 5, (32) 18+ Chi twood 1981Grays Harbor 10 Wendler et al. 1954lo+, (-30) 12 29+, (489) Simenstad and Eggers 1981- - - - - - - --I- and + indicate less than and greater than the values given, respectively.littoral channel habitats to utilizationof pelayic, mainstem channel habitatsgenerally occurs when both juvenile chumand chi nook (fry) reach 50-60 mm FL (Levyet al. 1979; Healey 1980; Levy and Northcote1981, 1982; Keimers 1973; Simenstadand Eggers 1981). A number of mechanismsaccounting for this shift in habitat utilization have been proposed, incl uding salini ty and temperature preference (Dun ford1975; Healey 1980), behavioral responsesas a function of density and size (Reimers1973; Myers and Horton 1982), and theavai 1 abi 1 i ty of preferred prey oryanismsor ontogenetic chanyes in food habits(Simenstad and Eggers 1981; Simenstad andSalo 1982).Individual residence times in themainstem channels vary as a function ofthe period in the salmon miyration, sizeof the fish, and density of the estuarinepopul ation. Juveni 1 e pink salmon appearto emigrate directly out of the estuary,since no records of pelagic residence areavailable for Washington (lable 6.4) orother estuaries in the region. Juvenilechum may reside in pelayic habitats ofmainstem channels for an additional twoto four weeks (Table 6.4; Manzer 1956;Mason 1974; Healey 1979) but seldom occurin these environs when larger than 75-80mm FL. Healey (1979) also indicated thatjuvenile chums from the early portion ofthe outmiyrating popul ation resided in ttleNanaimo River estuary considerably longerthan those which entered the estuary laterin the outmigration. Salo et al. (198O),Simenstad and Salo (1982) and Bax (1982),however, have documented the opposite relationshipin Hood Canal, where migrationrates tended to be higher and residencetimes shorter for the earlier outmlyratingpopulation. Juvenile chinook (fry)may reside in estuarine channels 1 ongerthan six months, but residence is quitevariable among estuaries. Keirners (1973)identified five 1 ife history variationsin the population of fall chinook inSixes River, Oregon. The prominent type

esides in the estuary a relatively shorttime (eight weeks) before emigrating tothe ocean whereas a second type rearsalmost twice as long but is measurablyless abundant in the estuary (17% oftotal migrants); the latter life historytype, however, typical ly contributed over90% of the returning adults. The othertypes passed rapidly throuyn the estuaryeither as fry or as yearling smolts butwere seldom abundant. A1 though earl ierwork (Simms 197U) estimated brief, i .e.,10-15 days in spring and summer and 7-10days later in the year, residence tirnesfor juvenile chinook (fry) in the Colun~biaKiver estuary, rnore recent results (Natl .Mar. Fish. Serv. 1981) trom on-goiny narkand recapture experiments have indicatedextended residence from Apri 1 throuyhOctober. Residency patterns very simi 1 arto those documented in the Sixes Kiverestuary have also been described for juvenilefall chinook (fry) in Grays Harbor(Simenstad and Eggers 1981), the Ouwami shRiver estuary (Salo 1969), and the QuillayuteRiver estuary (Chi twood 1981).Chinook snio Its (year1 ing) probably appearin estuarine channels only transitional ly ,as no significant estuarine residencetimes have been described for this lifehistory type. Similar to yearling chinook,coho smolts also utilize estuarinechannels principal ly as corridors for directemigration to the ocean (SjolSeth1969; Simms 1970; Chitwood 1961; Natl .Ilar. Fish Serv. 1981), but residence timesas long as four to eight weeks have beendocumented (Grays Harbor, Simenstad andEggers 1981). No information on individualresidence times of sockeye smolts isavailable nor is there an indication thatthey utilize estuarine channels otherthan for their immediate migration fromlacustrine rearing habitats to the NorthPacific Ocean. In fact, the occurrence ofjuvenile sockeye in estuarine channelshas only been documented for the ColumbiaRiver (ktl, Mar. Fish. Serv. 1980, 1981),Fraser River (Northcote et al. 1979), andthe Quillayute River estuaries (Chitwood1981).Entry of adult salmon into estuarinechannels prior to their migration upriveroccurs essentially year-round, althoughthe maximum migration period is typicallybetween July and September (Table 6.3 and6.5). Although tirning of return is principallydetermined uy the genetic attributesof the different species and populations,external influences such as oceanictemperature and current patterns, preyresources and photoperi od add el enients ofvariability to the temporal distributionof returning spawners (Simenstad et al.1982b). Once in the estuary, fish mayaygregate in specific, "staginy" areasbefore initiating the final phase oftheir spawniny III~ gration; upriver movementsare probably stimulated by increasesin river discharge, changes in watertemperature and air pressure, and tidalcycles. As a result, residence time ofadults within estuarine channels, althouyhtypically brief, has been estimated torange from 1-6 weeks (Simenstad et al.1982b; Table 6.5) and the fish are oftensubjected to intense corn~nercial andrecreational exploitation in thesechannel staying areas duri ng this period.Other anadrornous fishes include Americanshad, longfin smelt, eulachon, andstriped bass. Of these, American shad andstriped bass are distributed principal lyin the southern coastal estuaries of theregion, a1 though striped bass have beenreported in Puyet Sound (Mi 1 ler andBorton 1980) and American shad occur inapparent spawning popul ations in severalPuget Sound estuaries--Nooksack, Skagi t,Sti 1 layuamish, and Skykomi sh (Mi 1 ler andBorton 1980). These latter two specieswere not oriyinally indigenous to thewest coast and have continued to expandtheir distribution from San Francisco gaywhere both were introduced in the late180U's or from the Columbia Kiver whereshad were introduced in 1885-1886 (Hart1973; Wydoski and Whitney 1979).American shad are the rnore prominent,especially in the large coastal estuariessuch as the Columbia Kiver and GraysHarbor. In the Columbia River the adultmigration through the estuary is usuallyinitiated in May, coincident with 13-18OCwater temperatures (Leggett and Whitney1972), and peaks in June and July. Juvenile (young-of-the-year) shad enter the

Table 6.5. General estuarine run ti1:iing and estilllated il,dividua] residerice til:les foradult Pacific salrilorl in 'lashinnton State estua,.ies (froln Silllenstad ct a1 . 198:'b).-- ---- - _.fimdfgd -i;;divi-d;al-resraence-P--Run timing 1(tine in days)Seec i es eik ~-d;;@---- Ka. x.rm-.m----- -- ---- -.--- - -- - -- -- -- -- ____--______._._____--I_"_.-___----------KirrcnumBa ta souic2--- -Pink Late July-early Aug. June-Sept. 6.9 13.7 Barker 1979(only in odd years) 8.1 32.2 Barker 1979Sockeye July June- Aug. -Coho Late Oct. Sept.-Nov. 13.0 40.0 Eames et dl. 1981;in press9.2 14.7 Barker 1979Chi nook Late Aug.-early Sept. July-Sept. 27.4 39.6 Stauffer 1970Mi d-0ct.-early Nov. Sept.-Dec. 11.0 40.0 Eames et dl. 1981;in press3.0 6.8 Rarker 197913.0 20.6 Olney 1976f I*,,:,vdr' >us Wdr:lillg toll Depdt't:ileflt of Fisheries (ifarves t Yandc]cr?ct~t nivision) d??n sources.estuary beginniny in Auyust and residethere, reaching maxi~rlunl density inNovember and December, unti 1 eniigrat ingto the ocean as yearlinys when the younyof-the-yearshad become nurnerous in October(Ha~riniann 1981; Natl. Mar. tish. Serv.1981). Simenstad and Eyyers (1981) reporteda rnaxi~num sustained residence ofat least 10 weeks, but their sampling didnot extend beyond October.Lonyfin smelt and eul achon are anadroriiousosmerids that mi y rdte throuyh Pacif ic Northwest estuaries as adults durinywi nter months, but solrie spawn ing Itlay actually occur in the more freshwater-dominatedsysterris such as the Columbia Kiverestuary (Mi si tano 1977; kt1 . Mar. Fish.Serv. 1981). Up to three different ageclasses of longtin smelt, dominated bythe young-of -the-year and year1 inys, wereidentified in the Colurnbia River estuary(Iktl. Mar. Fish. Serv. 1981). ~esidenceuf young-of-the-year was sustained fromJune throuyh the winter of the followingyear but was confused by the influx ofspawniny adults in the fall. Occurrenceof lonyfin smelt documented by simenstadand Eggers (1981) indicated more ephemeraldistribution of juveniles in GraysHarbor, at least in the inner reaches ofthe estuary, where three major influxes(the longest residence lasti rig 3 weeks)were evident betweerr March and October.Juvenile longt in s~rrel t also appear touti 1 i ze estuarine channels within PuyetSound (Duwa~rii sri, Skyko~rii sh, St i 1 1 i yuamish, Skagit and Nooksack Kiver estuaries;Miller and Borton 1980) and the Straitsof Georyia (Fraser River estuary; Northcoteet al. 1Y7Y), but they are much morecolilmon in the nerit'ic hdbi t"ats outsidetne estuaries proper (Stuber et dl.1973a; Miller et al. 1978, 1980; Fresh1979). Colrlpared to lonytin smelt, eulachonare so~r~ewhat 1 ess prominent i nestuarine channels, but both adults dndjuveniles are comrnon in estuaries ofrivers with spawniny populations, notablythe Colunibia Hiver (Smi ti1 and Saalfield1955; Haertel and Osterberg 1967; Natl .Mar. Fish. Serv. 1981), Fraser Kiver(McHugh 1939, 1940; Nortncote et al.1979), Squamish Ki ver (levy and Levi nys1978), Nooksack Kiver (Mydoski and Whitney1979), and Puyal ]UP River (CommencementBay, Miller and B0rton 1980) estuaries.AI though eul achon were reported to occurin tirays Harbor (Smith et a1 . 1980), nonewere captured duriny the extensive samplinyin that estuary described by Simenstadand Egyers (1981). Their occurrencein the Columbia River estuary js concentratedbetween February and May as a re-

sult of the migration of adults into the where they are as abundant as, or secondestuary and its tributaries and the down- in abundance to, the predominant Pacificstream drift of the yolk-bearing larvae herring larvae, but they are relativelythrough the estuary (Misitano 1977; ktl. rare in and north of the Columbia RiverMar. Fish. Serv. 1981). Despite this estuary.brief occurrence, Mi sitano (1977) listedeul achon as the second most abundant (19%Occurrence of ichthyopl ankton in theof total) larval, post-larval, and juve- region's estuaries is essentially ani le fishes in the Columbia River estu- winter-spring phenomenon, both in termsary. Prolonged residence within the of species richness (as many as 18 speestuaryappears to be minimal, however. cies per sample) and density (maximabetween 0.4 and 11.0 larvae m-3) in theAlthouyh only a relatively recent coastal estuaries. Tidal and die1addition to the anadromous fishes in the variation can be considerable and isregion, striped bass have become promi- often associated with location in thenently established in Coos Bay (Roye estuary; for example, tidal excursion of1979) and Umpqua River estuary (Mu1 len water inasses with particul arly high densi-1972, 1974; Ratti 1979a). Residence of ties of larvae can result in high catchesadults in Coos Bay may be continuous, during ebb tide periods (Pearcy anda1 though some may emigrate to the ocean, Myers 1974), especially in situationsand then migrate upriver to spawn between where shal low sub1 i ttoral and 1 i ttoralMay and July. Juveniles spend the first flat habitats are sources of larvae.year in ri verine habitats before immigra- Contributions of predoini nantly offshore,ting to the estuary. i.e., marine, species into the moresaline, lower reaches of the estuaries6.2.3 Ichthyoplankton also promotes higher species richness inthese regions. Pearcy and Myers (1974)In addition to those pelagic fishes itemized 19 taxa of fish larvae in Yaquinawhich are found in estuarine channels Bay which were characteristic of offshorethroughout their development from 1 arvae assemblages, as compared to ten taxa assoorpostlarvae to at least juvenile stag- ciated with bay assemblages, and Misitanoes, approximately 17 species also occur (1977) documented a steady decline in theas prominerit ichthyoplankters but move number of species of larval, post-larval,either into other microhabi tats within and juvenile fishes collected at progressthechannels or into adjacent estuarine, ively more estuarine to riverine l0camarine,or riverine habitats (Table 6.2). tions in the Columbia River estuary.Those which undergo ontogenetic transpositionfrom pelagic to demersal modes with- While many of the same assemblagesin the channels include Pacific tonlcod, and patterns that occur in the coastalsnake prickleback, saddleback gunnel , estuaries may characterize inland esturockfishes,yreenlings and lingcod, all aries, there is no comparable informationfour species of cottids and four species on the ichthyoplankton in estuarine chanofpleuronectids. Of these, prickly, nels inside of the Strait of Juan dePacific staghorn, buffalo scul pins, and Fuca. Blackburn's (1973) documentationsnake prickleback are the more common and of the ichthyoplankton assemblages offabundant(Eldridge and Bryan 1972; Pearcy shore of the Skagit River delta indicateand Myers 1974; Mi si tan0 1977; Simenstadand Eggers 1981). bong those whichthat taxonomic simi 1 aritieswith the addition of severalmay exist,species ofsettle out in adjacent habitats, the baygoby is the most prevalent as an ichthyogadids(Pacific cod, Gadus macrocephalus,and Pacific hake, ~e-cius productus)p1 ankter before it assumes its ultimate and pl euronectids (slender sole, Lyopsetjuvenileand adult residence in shallowsub1 ittora] and 1 i ttoral f 1 at habitats.%.exilis), but spatial or tempormtri buti on and abundance of 1 arvae withinBay goby larvae are especially abundant the estuary's channel habitats were notin the more southern coastal estuaries assessed.86

CHAPTER 7BIRD ASSEMBLAGES OF ESTUARINE CHANNELSAlthough some of the resident andmigratory bird species utilizing PacificNorthwest estuaries do not frequent channelhabitats, most of these estuaries'avian fauna occupy channels at some timefor foraging and roosting, and some aredependently bound to the habitat throughcritical food web 1 inkages. Severalspecies, notably the migratory waterfowl ,can occur in such high abundance thatthey play significant, though oftenseasonal, roles in the food-web dynamicsof these estuaries.Adopting Peterson and Peterson's(1979) classification of 1 ittoral flatbirds into ecological assembl ayes or"guilds, "5 estuarine channel birds havebeen categorized into four assemblagesprimarily as a functon of their foragingbehavior: 1) shallow-probing and surfacesearchingshorebirds; 2) waders; 3) surfaceand diving waterbirds; and 4) aerialsearchiny bi rds.Habitat-specific inventories and descriptionsof birds of Pacific Northwestestuaries are rare and typically inadequatein the scope and resolution of thedocumentation of bird di stri bution, abundance,behavior or ecology. Jones andStokes Associates, Inc. (in prep.) is themost complete in terms of temporal (seasonal) and spati a1 (habitat, areal ) documentationof birds occurriny in any oneestuary (e.y., the Columbia River). 0th-5~ will refrain, however, from usingthe term "guild" because of the assumptionof common exploitation of an investigator;defined resource (Root 1967; Jaksic1981), opting instead for "assemblage,"which is more broadly defined as a groupof syntopic related taxa.er estuary-oriented accounts includeYocum and Keller (1961), Ives and Saltzman(197O), Smith and Mudd (1976a), Seaman(1977), Crawford and Edwards (1978),Peter et al. (1978), and Edwards (1979).More taxa-speci fic documentation includesWetmore (1924) on grebes, Henny and Bethers(1971) and Bayer (1978) on great blueherons, Erskine (1971) on buff1 eheads,Couch (1964) on sandpipers, Pen1 and (1976)on terns, and Vermeer and Levinys (1977)on ducks. General references descri bi nyspecies of estuarine birds and some oftheir habits in Pacific Northwest estuariesinclude Gabrielson and Jewett (1940),Jewett et al. (1953), Eaton (1975), Salo(1975), Manuwal (1977), and Simenstad eta1 . (1979a). The most authoritative,quantitative information, that includedin Wahl et a1. (1981), encompassednorthern Puyet Sound and the Straits ofGeorgia and Juan de Fuca but seldom coveredor ditferentiated bird assemblagesin true estuarine channels.Synthesis of these references and ofpertinent coastal inventories (U. S. Dep.Interior 1971; Monroe et al. 1974; Kreag1979a, b, c; Ratti 1979a, b; Roye 1979;Starr 1979a, b; Proctor et 31. 1980; Beccasioet al, 1981) indicate that 59 speciesof birds are common to the region'sestuarine channel habitats, 23 of whichcould be considered prevalent (abundant)(Table 7.1; Fig. 7.1, 7.2).7.1 SHALLOW-PROBING AND SURFACE-SEAKCHINGSHOREBIRDSCharacteristic of their foraging onor within sediment surface layers, birdsof this assemblage occupy shore1 i ne envi -rons constituting the boundaries betweenchannel and other estuarine habitats.Comprising slightly more than 25% of the

Table 7.1. Itemization and characteristics of birds comon to estuarine channels ofthe Pacific Northwest, organized by assemblage.TaK- -- --- - ---I-- 3-ann T----- SaTTnnyTeTi;aX me- '-%blage- --- -(conmon - name) - --habi tats1 associ ations2 history characteristics3 ------- --Shal low-problng and Haernato us bachmnl M E 0 -8surface-search1 ng o d b ~ a c oystercatcher)kshorebirds*~haradrtus alexandrt nus M-B0-B; Seasonal transient(5nowyoTerl-C. seml alrnatus~se*orcr)M-B R -E 0-B; Seasonal transientPluvial is s uatarol ama-1 &-p~r)M-BR-E0-B;Seasonal transientM-BR -E0-BM-BR-E0-B;Seasonal transientM-BR-E0-BL scolo aceus~io~&3owlA hrlza vlr ate~&*ifaP--- -tcherlM-Bn,sArenarla inter resM,S~ ~ ~ U Z Y O ~R-EM-E0-E0-B0-8; Seasonal transient0-B; Seasonal transient*cat ldrl s a1 baTSiinnGFfl ngl-M-BR -E0-8; Seasonal transientM-B0; Seasonal transientM-BR-E0*c. maurl M-B R -E(~6s~e%-sandplper)C. minutllla M-B R-EReTsXnii per )Ph;arop;s 1 oba tus M M-E-nec ed phalarope)00-80,F-PK;Seasonal transientWaders*~rin~a wl anoleuca H-0 R -E'IT;rc?atci;~T&wTeigsF-0;Seasonal transient*~rdea herodias M-B R-ETr;F6StTiTGTTiiron)0-PSBubulcus I blsTFa'FKTeeFet)R-EF-PSCasnerodius a1 busTGreat egretr-S9-retta thul anowy eg-M-BM-B(continued!R-E0-PS0-PS

-Table 7.1. Continued.Taxa ---Tli%ini - -TaTfnTQ-- - - e evant lffe- ---Assemblage ( comno n name) habitats1 associations2 hlstO~1characteri~ti~~3 'Surface and diving *~echmophorus Occidental iwaterbirds mestern grebe) R -E 0-PS;;dfceis auri tusorne gG&'l--ke%&%?grebe) M,S R-EF-ps; seasonal transient0-PS; seasonal transientP. nigricollisEared grebe)R-E 0-PK; Seasonal transienthala lac roc or ax auri tus MsS R-E 0-PS7Doubl e-crested0Pm)rant)* b e ~ m r a n t ) M.S M-E F-PSergus us mer anser M-B R-E 0-PSKGiEn me:ganser)M. serrator M-8 R-E F-PS; Seasonal transientTRea-breasted merganser)M M-E 0-PS; Seasonal transientCepphus columba M M-E F-PS(Pigeon @71Ekt)Cerorhinca monocerata(Rhinocerosauklet)M-EBrach rarn hus mannoratus M H-E F-PSm e rBranta bernicl a s.6 R-E 0-H; Seasonal transient-m)-*~nas platyrhynchos M-8 R-H 0, F-H; Seasonal tranmaTlard)sient; primarily roostingin habi tatA. acuta M-0 R -M 0. F-H; Primarily roost-T~oZliFn pintail )Ing in habitatA. crecca M-B R -M 0, F-H; Seasonal tran-TGrGGXnged teal )sient; Primarily roostingin habitat*A. a~nericanaTherican wigeon)M-B0. F-H; Seasonal transient;Primarily roostingin habitatAythya valisineria(Canvasback 1M-BR-M0, F-H; Seasonal transient;Primarily roostingin habi tatA. marilaTGrFZiF"-scdup )M-S R -E F-8; Seasonal transient(continued)89

Concluded.niT--' TinTfy---'---- - Pelevatt 1 i fe ---'-Ise:ge ------~-.-------~--_----_------------ (common name) habl tats1 associatfons2 --. hlsto!y characte?2st~c?Table 7.1.-'-Tar- ------.-Surfac~ dnd drviny 'A, afffnlswd terb t rds - cnnt 'd. ResrCerf?ICaup)M-S R-E 0. F-B; Seasonal transient.Primarily roostingin habitatBucephela clanpule M-R R-E B-0; Seasonal transientKooibniijaTiicriG~P70. albeolarnurtl e ~ ~ i d )M-I3 R-E F - 0'Relanl tta fusce M-§ R -E F-B; Seasonal transient7Zlh'fT e-iTn33ddS~ o t er)'M. perrpfclllata M-S R -E F-BTSurT scotE-i.T--'Acrtal-searching birdsCrr 1.alc ond-trj&tshrr)'lsrur 91 rucescrnr M-H R -E F -0~aucou"s=%Tnghd 9111 1)L. occfdentalis M-8 R-ETLer t'i;riT gun T 'I. calf forn$cus 4l-R R-E F-B; Seasonal transientlGaT irofifL-giu7111. drlawarensit M-R R -E F-0; Sesronal transientmi ng-bTT7ad gull1. LeecCrl"p~t~i M-5 R-E F-B, Learonal tran~icntTiicc~rannT.~u\ I )'L. phftabelphta n-5 M-E F -PYIBanipYif$ s girl 1 )M,S W-E 5-PS; 5casonal transient*s. casptaFCaspidn tern)M,5 M-E F -P\; kasonal transientPel ~c .%nus occ1denf.d~ 1 \ M P-E 5-PS; 5easonal transientpF;i,-T6"l Fini - -- . -Stercorarlus paras!_tljfu~ H-B R-E F-PS, K. Searondltransient--. -.- -- - > * - ---?h+a

Anab plalyrhyn~hnsA dmBrh^BndLITTORAL FLATSSUBSIMARY CHANNELSBLlNCJ CHANNELSFig. 7.1. Representative i 11 ustraii on of common bird assemblages of cstuarine channelsof the Pacific Northwest.common species and five of the prevalentspecies (three families in the orderCharadri i formes; Haematopodidae, Charadri -idae, and Scol opacidae) , these shorebirdsare typically seen actively feeding inthe substrate along the shorel ine, particularlyat high tide when littoral flathabitats, the preferred foraginy habitatof most, are inundated. Due to the yenera1lack of daylight minus tides betweenSeptember and February, much of the fallwinterforaging by this assemblage isconceritrated closer to and about channelshore1 ines. Some (kerican bl ack oystercatcher,snowy plover, whimbr~l , bothdowitchers, dunlin, knot, sanderling)appear singly or in small, looselyassociated groups whil e others (sandpipers,surfbird, ruddy turnstone) occurin dense, tightly associated flocks.Considerable habitat parti tioninyresults as a function of the heterogeneityof shoreline substrates. Thus, currentand wave exposure which influencessediment characteristics of channelshorel i nes deternlines, to a 1 arye extent,the species composition of this assemblaye. For example, black oystercatchersare typically found along rocky cliffs,headlands, and jetties in the euhalineregion of those estuaries which possessthis habitat (predominantly in Oregon) ;dun1 ins. western sandpi yers, sander1 i ngs ,and knots appear commonly on exposed sandbeaches in the lower reaches of the estuaries; and whimbrels and dowitchers characterizethe more protected, inner baysand flats. Tidal fluctuations affectingthe avail abil i ty of preferred foraginghabitats and microhabi tats, however,

. .t-lq. 7.7. Representative avifauna of estuarine channel habitats in the Pacific Northwest:A) feeding dowitchers; 6) sprin~ flock of western sandpipers, dunlins, and shortbi.1led dowi tchcrs; C) feeding nmle northern pintai 1s; D) adult CGlIlrlion loon (Gavi?. i1111ner)ir winter !;lui!iage; E) fll1 +lock of California and tieernlann's gulls; and, F) adult aonaparte';gill1 in winter pl~ii~~age. Ail photographs courtesy of Dr. Dennis Pau!son, LJniversiiyof Washington.

induce considerable ~lioveinent about theestuary and many species periodicallyfrequent a diversity of habitats. Assuch, considerable spatial overlap inforaying space is imposed upon theseshorebirds, which may be responsible forthe evolution of diverse feeding behaviorsand bi 11 morphologies (Kecher 1966).Distribution of the assemblayethrouyhout the region is relativelyuni forni wi th some exceptions (Beccasio etal. 1981). For example, snowy ploversare concentrated along the marine marginsof the southern estuaries and dun1 ins appearmore in the central coastal estuaries(1.. Tillamook Bay, Willapa Bay,Grays Harbor), and, in general, the migratoryspecies are more commonly encounteredin abundance along the coastal estuariesthan in the inland estuaries, which areinore re~iioved from the mainstream of thePacitic Flyway.Approxiinately a third of the assemblayeare migrants and their abundancestypical ly reach maxima in spring (Apri 1 -May) and fa1 1 (September-November) , whenthey are migrating through the PacificNorthwest. Intermediate 1 eve1 s of abundancein the winter are associated withoverwinteriny of soine species in the estuaries.This variation is illustrated bythe corrected aerial estinlates of totalshorebird abundances in Grays Harborbetween September 1974 and October 1975which fl uctuated between averages of65,833 in spriny, 19,700 in summer, 52,500in fall and 21,533 in winter (Smith andMudd 1976a). Similarly, Jones and StokesAssociates, Inc.'s (in prep.) summary oftheir 1980-1981 CKEDDP studies of theavifauna in the Columbia River estuaryindicated densities of "peeps" (confinedto the "key" species of dunlin, sanderling,a d western sandpiper) as high as378 km- 9 in spring , 766 ~J-I-~ in fa1 1, and961 kin-2 in winter, but peeps arevirtually absent in the summer. Distributionof the assemblage was also broadest,essential ly covering the whole estuarybut concentrating on mid-estuary, in thespriny and was more restricted in thefa1 1. Significant overwintering was observedonly at one site in the upper estu-ary, although "peep" density along a linear transect was estinldted at 337 km-Iduriny that period.7.2 WADERSThi s assernbl age, confined to bi rdsthat wade throuyh shal low-water portionsof the channel in search of invertebrateand fish prey, is composed of two yroupswhich are quite di fferent in distributionand ecol oyy. Greater ye1 1 owl egs (Fami lyScolopacidae) forage a1 ony channel shoresand shallows in water 5 to 10 cm deep andthus are found within channel haoitatsonly when blind channels are tidally dewatered.Like inany of the other shorebirds,they are seasonal transients whoare most abundant in the reyion's estuariesduring spring and fall niiyratoryperiods.Great blue herons and eyrets (tamllyArdeidae) are estuarine residents thatnest in wetland and adjdcent upland, andforage in marshes, littoral flat, andchannel habitats in waters 41 m deep. Inchannels, this includes shore1 ine andslope areas of iirainsten~ channels and shallowsubsidiary and bl ind channels throughoutthe estuaries. Great blue herons aredistributed ubiquitously throuyhout theregion while eyrets are locdted principallyin the coastal estuaries of northernCalifornia and southern Oregon (Beccasioet al. 1981). The density of herons inthe Columbia Kiver estuary peaked atalmost 3 km-1 of linear transect surveyedduring the summer months due to recruitmentof young, but averaged between 1 and2 km-1 during other seasons. Althoughdistributed through all estudrine regions,herons tended to be concentrated In thecentral (i e. , 01 igohal ine-polyhal ine)region ot that estuary. Part of thisheterogeneity was due to the proximity toheron nestiny colonies in the vicinity otYounys Bay, Karlson Island, Ryan Island,and 8rown's Island (Jones and StokesAssociates, Inc., in prep.). Much higherdensities have been observed on the basisof linear shoreline; as many as 30 to 50immature herons have been observed perlinear km of shoreline in Grays Harborduring the summer (Dr. Dennis Paulson,

Burke Mus., Univ. Wash. Seattle, WA;pers. comcn. ) .7.3 SURFACE AND DIVING WATERBIRDSAnothergredorninant bi rd assemblagefound in estuarine channel hahi tats isthat of the surface and diving waterbirds,which constitute over 40% of both thetotal comnon and prevalent species (Table7.1) and include members of four farnil ies(Podicipedidae, grebes; Phal acrocoracidae,corntorants; Anatidae, waterfowl; andAlcidae, alcids). Unlike birds of theother assembl ages , they ut il i ze the channelwater directly for hoth roosting andforaging. A1 though a1 1 roost on openwater, during Feeding some are conf ined tocertain channel microhabi tats by the constraintsof their foraying behavjor andprey preferences. Benthic herbEvorez(brant, mallard, northern pintail, greenwingedteal , canvasback) and carnivores(doubl e-cres ted curr~iorant, horned andred-necked grebes, qreater and lesserscdup, contrliori goldeneye, buf t 1 enedd,whi te-winged and surf scaters, p iyeongull lernot) teed in shal low, ctldnnel slopedrrds where yl ant and anillla1 taud resourcerdre wrthln their resy~ctfve dlvlngranges, whi l e pet dgic piscivor~s (pelagicCOnlloraRt, conlnon and red-breasted IrrPryanser,Bonaparte's gull ) and plankt tvores(eared grebe) tend to congreyate d 1 ongtidal fronts whlch congregate thelr prey.Same species, ydrtr culariy tne yiscivorousspcles, are turrner restricted tocrlaflnrl s 1 n the euna l inr-mesoha1 i n reglansot the estuary. Smith and Mudd(19fbi3) il lustrated ttw areal dlstributrarlut seabirds (inciudlng rlllnocerosduklet~, coti\i\ion ttiurres, warnlcid rtlurrel~ts,plyeon yui 1 Ie~tlots) 10 (;rays Harborto be conllncd to rtldnnel hdbttdt li1 tll~outer castudry wllere water ciepth was qreaterthan O tri relatlve to MLLW (Ely, 7.3).Ul~trlbutlon~ of pelaytc cormorant anr!surt scoter were sirni 1 ar ly concentrdtedin lower dnd mid-estuary regions ot theC~lunlirta River estuary, while otherspecles (ma11 drd, Anterican wlyearl, andcaarri

Fig. 7.3. Seabird (primarily rhinoceros auklets, common murres, marbled murrelets, andpigeon guillemots) distribution in Grays Harbor, Washington, October 1974 to September1975; stippled area indicates littoral sand or mudflat habitat and hatched area indicatesseabird occurrence (figure from Smith and Mudd 1976a).7.4 AERIAL-SEARCHING BIRDSAerial-searching birds include bothterrestrial (be1 ted kingfisher, swallows,osprey, bald eayle) and waterbi rds (gul ls,terns, and brown pelican) which fly overand along channels whi le foraying forprey over, on, or just within the watersurface. Waterbirds also roost on thesurface.Be1 ted kingfishers, ospreys, andbald eagles all require perches in theproxiini ty of their common foraging habitatand thus are less prevalent or absentover channels in large expanses of openwater such as occur in the lower regionsof many estuaries. In the Columbia Riverestuary, for example, the di stri butionand abundance of bald eagles is centeredin the central region of the estuarythrough most of the year (Jones and StokesAssociates, Inc., in prep.). The proximityof foraging habitats to nesting sitesmay also restrict the effective distributionof these birds along the estuary.Gulls and terns, however, are muchmore widely distributed through tne estuariesas theJ r a ~ i d cover l ~ broad expansesof open water during their feeding foraysaway from estuarine breeding colonies.Much of tnis wide aerial distribution isdue to the relatively dynamic nature oftheir prey resources, such as macrozooplanktonand small, schooling fisheswhich occur sporadically with shiftinycurrents and tidal fronts throughout theestuary; tidal inundation and exposure ofbenthic and sessile organisms alony channelshores also contributes to movementof gulls which prey upon these organisms.

While the terrestrial-associ atedbirds of the assemblage are estuary residents,both mew gulls and the two ternsare seasonal transients, a1 though inopposite patterns. Mew gulls, like mostof the waterfowl, migrate out of the region'sestuaries during the summer. Themaximum abundances recorded in Grays Harborbetween October 1974 and September1975 occurred in December though April(maximum of 1.4 km-1 along a channeltransect in upper estuary in March) andthe gulls were absent froin May throuyhJuly (Smith and Mudd 1976a). Jones andStokes Associates, Inc. (in prep. )reported maximum mew gull densities of193 km-2 in fall 1980 and 400 km-2 inwinter 1980-1981 in the Columbia Riverestuary. Common and Caspian terns aresummer immigrants into the large coastalestuaries and Caspian terns breed in largeestuarine colonies throughout the region(Beccasio et al. 1981). High densitiesof common terns occur in Grays Harbor inMay (2.6 km-1 along channel transect inupper estuary) and equally so in September.Caspian terns, which breed onWhitconib Island in the lower estuary fromMay to October (Penland 1976), are mostabundant (18 km-1) in channel habitatsduriny July when food requirements forfledglings are at a maximum (Smith andMudd 1976a). The density of Caspianterns in the Columbia River estuaryreached %93 km-2 during summer 1980censuses by Jones and Stokes, Associates,Inc. (in prep.).As the "Cal i fornia" subspecies, thebrown pelican is an endangered specieswhich occurs in small aggregations ofiirimatures as tar north as Grays Harborand is a fa1 1 (Auyust-September) occupantof the euhaline regions of a number ofthe coastal estuaries to the south (WillapaBay, Columbia River, Coquille, Chetcoand Humbolt Bay) (Beccasio et al. 1981).

CHAPTEK 8MAMMALS UF ESTUAK IN€ CHANNELSTerrestrial, aquatic, and marine mammalsutilize estuarine channel habitatsto varying extents and for various purposes.A1 though rrrembers of adjacent wetlandor upland communities, terrestrial mammals periodical ly forage along the shoreline boundaries with channel habitats.Aquatic marnrnals actually uti 1 i ze channelsfor much of their principal foraying.Compared to terrestrial and aquatic mammals, marine marnrnals occupy channels extensively,some exclusively, for foraging,movement, migration, restiny, andreproduction. Other than rnan, they constitutethe predominant ~roportion of thetertiary consumer level (see Chap. 9).One terrestrial (procyonid), fouraquatic (one each castorid, cri cetid, capromyid,and mustelid), and four marine(all pinnipeds) mammals are common tochannel habitats in Pacific Northwest estuaries(fig 8.1; Table 8.1). In additionto these, other marine mmmals such asorca or killer whale (Orcinus E) , har-IFig. 6.1. Representative illustration of common mammal assemblages of estuarine thannelsof the Pacific Northwest.i

Table 8.1. Itemization and characteristics of terrestrial, aquatic, and marinemammals common to estuarir'e channel habitats in the Pacific Northwest.---Re 1 evantChannel Salinity 1 i fe hi storyTaxa habitats1 associations2 --- characteri stics3Terrestrial :Procyon 1 otorm n rAquatic:Castor canadensi s(American beaver )-Ondatra zibethicapiizzt)-Myocastor coypus-r-)Lutra canadensi sm d i a n river otter)Marine:K-Es ,B R-0S,BS,BM-BR-MR-MR-E0-HO-H0-H0-ECEumetopias jubata M,S K-E F-PC(Northern sea 1 ion)Zalophus cal i forni anus M, S R-E F-PC(California sea lion)~hoca vi tul ina richardiK-EF-EC(Harb0FTzJ-J-Mirounga anyustirostrls M P-E F-PC(Northern elephant seal)IIII= Mainstem; S = Subsidiary; B = t31 ind.2~ = Riverine; 0 = Oligohaline; M = Mesohaline; P = Polyhaline; E =Euhaline.30- = obligate; F- = facultative; EC = epibenthic carnivore; PC = pelayiccarnivore; H = herbivore.bor porpoise (Phocoena phoccya), graywhale (Exchrichti us robustus and minkewhale (~alaenoptera acutorostrata) havebeen reported sporadical ly in the region ' sestuaries. As with the avian assemblages,comprehensive documentation of mammal assemblagesin the region's estuaries isrelatively recent and limited to thecoastal estuaries in the vicinity of theColumbia River, e.g., Grays Harbor, WillapaBay, Columbia River estuary, TillamookBay, and Netarts Bay (Smith and Mudd1976b; Howerton et a1 . 1980; Dunn et a1.1981; Beach et al. 1981) and in the lessestuarineenvirons of northern Puqet Soundand the Strait of Juan de Fuca (Everitt1980; Everitt et a1 . 1980). Quantitative(population sizes and dynamics) studies ofterrestrial and aquatic mammals in PacificNorthwest estuaries are rare or nonexi stent.Assemblage accounts of distributionsand population assessments of marine mammals, however, have been available sincethe 1940's (Scheffer and Slipp 1944, 1948;Manzer and Cowan 1956; Cowan and Guiguet1965; Bigg 1969; Pike and MacHskie 1969).

Extensive population biology and ecoloyystudies ot pinnipeds in estuarine habitatshave occurred duriny the past twodecades (Pearson 1969; Pearson and Verts1970; Mate 1975; brow^ and Mate 1979;Calanlbokidis et al. 1978, 1979; Brown1980; t3owl by 1981; Koffe 1981). i3ecassioet al. (1981) included these commoninarnmal species in their colnprenensiveecological inventory of the PacificCoast.8.1 TEKKESTKIAL MAMMALSRaccoons are one of the few terrestrialmammals which trequents channelhabitats in conjunction with their principaluse of adjacent littoral tlat, saltand freshwater marsh, and riparian swamphabitats. Utilization of the channel isalniost exclusively contined to foraginyfor shal low-water fauna. Feeding periodicityand intensity is principally a functionof tidal cycles. A1 though raccoonshave been observed feeding during bothday- and nighttime, they appear to prefernighttime low tide periods when they cansafely foraye across littoral flats(Smith and Mudd 1976b; Dunn et al. 1981).Thus feeding activity tends to be seasonalin nature, i.e., more intensive in falland lowest during spring. Raccoons in theColumbia Ki ver estuary have been observedthrough all estuarine regions, from theeuhaline region of the Ilwaco Channel tothe marsh channels of Puyet Island, althoughpeak observations occurred in thecomplex system of islands and channels inCathl amet Bay (Dunn et a1 . 1981).8.2 AUUATIC MAMMALSAmerican beaver are common only insmall subsidiary and blind channels whichi ntersect freshwater marsh and riparianhabitats, particularly si tka willow (Sal ixsi tchensi s) , creek dogwood (Cornus stolo--1 nifera 'or similar habitats in riverinemesohalinemarshes such as the CathlametBay area of the Colunbia River estuary(Wash. Dep. Game 1981). Extremely smallchannels may be dammed and permanentlyoccupied (denning and resting) by beaverin some instances.Muskrat have a broader spectrum ofhabitat utilization than beaver, beingmore common in the sedge (Carex spp.),horsetai 1 (Equi setum spp. ), and bul rush(Sci rpus sp-and freshwater habi -tats in addition to the riparian habitatsoccupied by beaver (Smith and Mudd 1976b;Wash. Dep. Ga!ne 1931). Denning and resting,however, a1 so occur in close associationwi tti steep-sided estuarine (principally subsidiary and b1 ind) channel sadjacent to or in these habitats and, assuch, cor~stitute critical habitats forthis species (Dunn et a1 . 1981). Feedingand other activities almost always occurless than 60 ni. from the channel den andprincipally during high tide and nocturnalhours, perhaps to facilitate access tofeeding areas along the channel banks andto miniinize vul nerabil i ty to predators.Nutria habitats overlap somewhatwith those of American beaver in theiroccupation of marsh and riparian swamphabitats. In tne Columbia River estuarythe most common features of nutria habitatare compl ex steep-sided tidal channel systemswithin extensive high marshes (pri n-cipal ly reed canarygrass, Phalaris arundinacea/cattail, Typha sp.),whererprincipal forage plants (see Section 9.1)are readily available (Dunn et a1 . 1981).Unlike muskrat, nutria appear to maintainextensive home ranges (%U. 4 km2) containinyseveral habitats and to have no seasonalor die1 periodicity to their activity patterns,Among the terrestrial and aquaticmammals the Canadian river otter undoubtedlymaintains the highest utilization ofestuarine channels and is the only specieswhich comrnonly occupies mainstem channels.A1 though most observations of river otterin the Columbia River estuary were correlatedwith sitka spruce (Picea si tchensi s)and/or si tka wi 11 ow-domi nated forest, otterwere typically associated with complexchannel networks of tidal creeks andsloughs (subsidiary and bl ind channel s)which offered easily accessible, concentratedprey resources (cl arns, crayfish,and dernersal fishes) during periodictidal dewatering (Dunn et al. 1981). InGrays Harbor, river otter have been

observed only in tributary rivers andstreams, although it is assunled that theyutilize tne open waters of the estuary(mainstem channel s) to travel betweentributdries (Smith and Mudd 1Y76b). Ottersalso are relatively adaptable to tnepresence of man as lony as critical habitatand food resources are maintained;Cowan and tiui guet (1965) considered theinthe most numerous aquatic mammal inVancouver (U.C., Canada) Harbor.8.3 MARINE MAMMALSHarbor seals and Cali tornia andnorthern sea lions are both common andabundant in Pacitic Northwest estuariesa1 thauyh densities fluctuate seasonal lyas a function of feeding and breeding ~nigrations(Mate 1975). Northern elephantseals are less abundant in the region andnrr more concentrated seasonally in thesouthern extrane of the region. Whileall four species occur frequently incodstdl estuaries, northern elephantseals dnd Cali tornia sea lions tend to beless abundant in the inland estuaries ofPuget Sound.Northern sea l ions are most abundantin the reyion during the non-breeding seasonbetween late fall and early sprinyand, except for a snlall population alongttre outer coast during the summer (Everittand Jeffries 1979), are usually absentfrom the region frorn Mdy through July.Total counts of northern sea lions inWashinyton in 1976 and 1978 peaked at'L450 in February-March and at 2600 inSel~tewber-October (Everi tt et a1 . 1980).Hgt Beach et al. (1981) indicated thatnorthern sea lion populations in 1981vdried considerably among three haul outsltes in the vicinity of the ColumbiaRiver estuary; whi 1 e occupation of thesouth jetty site at the mouth of theriver was concentrated between Januaryand May, maximurn abundance at TillamookHead, Oreyon, occurred in May and Juneand did not occur at Three Arch Kocksuntil October-November. Much of thisvariation appears to be associated withshifts in preterred foraging habitat andlocation alony the coast duriny the summerand a potential movernent of sea lionsinto inside waters during the wintermonths (tveritt et al. 1980). Occupdtionof coastal estuaries often coincides withpredictably high concentrations of prey,sucn as eul acrion and spring chinook salmonspawni ng micjrati ons through the ColumbiaRiver estuary in winter and spring(Beach et al. 1981). Movement in and outof the estuary must be relatively dynamicduriny this period, ds no haulout areasare reported to occur within the estuary.California sea lions also occur inPacific Northwest estuaries during thenon-breediny season between Uctober andMay, when they move northward from oreedinysites at and south of San Miyue1Island, California. They follow the sameyeneral auundance di stribution pattern asthe northern sea 1 ion but are generallymore abundant in coastal estuaries andless abundant in inland waters (Everittet al. 1980; Beach et al. 1981). Everittet a1 . (1980), however, reported extendedhaul iny out of California sea lions athaulout areas in tne Port tiardner area ofPuyet Sound, a signi f icant expansion oftheir uti l i ration and abundance in insidewaters.In the Columbia Kiver estuary forayingCalitornia sea lions are numerousthrougnout the estuary during the springfish migrations, occurring as far upriveras Uonnevi 1 le Dam, a1 though no hduloutsites have been documented to occur withinthe confines of the estuary, This sea1 ion is credited with some fish and fishinggear damage irt the fa1 1 and is consideredto be the rnajor cause of year danagein the lower river and estuary during the1981 winter season (Beach et a1 . 1981).Of a1 1 marine mammals, the Pacificharbor seal is the most ubiquitous andabundant and is the only breeding pinnipedin the region (Scheffer and Slipp1944; Everitt et al. 1980). The State ofWashinyton is estimated to provide refuyeto over 7,000 harbor seals (Everi tt eta\. 1980). Beach et a1 . (1981) estimated5,000-6,000 harbor seal s present in theirstudy area between Grays Harbor andNetarts Bay, including at least 55 hauloutsites in the five major estuaries

COLUMBIA RIVER ESTUARYiWILLAPA3000BAY3000 -GRAYS HARBOR2000 -1000 -0J ' F ' M ~ A ' M ' J ' J ' A ' S ' O ' N ' D 'MONTHFig. 8.3. Maximum total abundance (aerial counts) ofPacific harbor seals at haulout sites in three of Washington'scoastal estuaries in 1980 (open symbols) and in1981 (closed symbols) (figure redrawn frm data of Beachet al. 1981).

the 1 atter of which include carnivoroustaxa such as Nephthys and Eteone. Whilesome organi srns('i.e,,Acmaem - gastropods)are assumed to graze discrirninatelyupon microal yae, it has com~nonly beenassumed tnat most capture and inyest foodparticles simply on the basis of size asa function of filtering or other feedinymorphologies. It has become readily apparent,however, that selective ingestionof food particles occurs, perhaps on thebasis of che~ni cal and/or physical composi -tion (1.. Tietjen and Lee 1977 fornematodes; Fauchald and Ju~i~ars 1979 for?olychaetes), and that "food" can becomposed ot a combination of benthicmicroalyae, detritus, pelagic phytoplankton,and meiotauna. More recent studieshave indicated that observed particleselection patterns are more the result ofthe mechanics of particle handling thanof behavioral responses to particle characteristics(Junlars et al. 1982; Tayhon1982). DOC, as we1 1 , may be assimi 1 atedin the feediny process or many depositfeeders (Stephen 1967; Steward 1979;Levinton 1980). The resulting finitepartitioning of food resources explains,within the constraints of temperature andsalinity tolerances, much of the disparatestructuring of benthic infauna assemblayesand standiny stock (see Section5.1) as a function of sediment grainsize, stability, and organic content(Sanders 1959).Motile epitauna are principallybenthic carnivores preying upon benthicinfauna or sessile epi fauna. Of the ninerepresentative species (Table 5.2), twaasteriods are obl igate feeders on sessilebivalves, yastroyods, barnacles, and seaurchins ; two crabs are tacul tative carnivoreson everything from benthic infauna,including rneiofauna, to fish; and threeshrimp species are obligate meiofaunacarnivores. Only two species, the crayfishPacificastacus leniusculus, andhermit crabs (Payurus-spp.), are, by theirdetri ti vory, prlrnary consulners.A1 though there is very 1 i ttle specificprey composition or feeding behaviorinformation on these consumers in estuarinechannels habitats, the diets of cran-gonid shrimps and cancrid crabs, the principal invertebrate secondary consumers i nthe community , have been exami ned fromseveral coastal estuaries. Prel iminaryanalyses of the stomach contents ofCrangon franciscorum collected fromdifferent locations of the Columbia Riverestuary in June 1481 (C. Simenstad, Fisn.Kes. Inst., unpubl. data) indicate that atthat time C. franciscorum was preying primarily on infauna and epi fauna, includingool vchaete annel ids. Coroohium s~o. amuhi -pods, and the harpacticoid copepod scottolanacanadensi s. There was l i ttle differencein diet amons the four locations fromwhich shrimp werQ examined. Three cranyonidsfrom Grays Harbor were also carnivorouson benthic infauna (Armstrony etal. 1982). C. franciscorum was found tofeed principa-lly on polychaete annel ids(15.4% trequency of occurrence) and unidentifiedcrustaceans (14.5%)) while C.niyricauda and C. stylirostris had prey3upon crustaceanr (12.7% and 11.5%. respect'ively)and small' bivalve mol lusds (19.0%dnd 7.72, respectively). A1 though notevident in these data, C. franciscorummay also be a major preditor on rnysids(i.e., N. mercedis), as has been reportedin the Sacramento-San Joaquin Riversestuary (Sieyf ried 1982).Prey composition of Dungeness Crabsin Grays Harbor varied according to predatorsize, die1 and seasonal cycles, andlocation in the estuary. In general, however,crabs (60 mm carapace width preyedprinlari 1 - Y upon . bivalve moll uscs (Tell inaspp., & arenaria, Cryptomya californ--- ica. Macoma suu.. ,. , Cardiidael and smallcrustaceans (amphi pods, harpatticoid copepods,tanai d~). Intermedi ate-sized crabsbetween 61 and 100 mm carapace widthpreyed equal ly upon small crustaceans,fish (1 ingcod, Pacific sanddab, Pacificsand lance, Pacific herring, Pacific tomcod,sand sole, shiner perch, longfinsmelt, Pacific staghorn scul pin), and1 arger crustaceans (Crangon spp. ; mudshrimp, Call ianassa cal i forniensis; Dungenesscrab), and 1 ess so on bi val ve mol -lusks. Large crabs >I00 mrn carapace widthpreyed predominantly upon fish, less onsmall crustaceans, and measurably l ess onlarge crustaceans and bivalves.

A1 thouyh there is considerable variationin opinion about food preferences(Coul 1 1973), epi benthic zoopl ankton canprobably be characterired as detritivores,as is often illustrated by their prominencein detritus a ~ ~ ~ m ~ lareas a t i ~ such nas the null zone (see Section 2.5.1). Assuch, they may play a critical role inthe initial biological (fragmentation)conditioning of detritus (see Section4.4) Harpacticoid copepods, in particular,have been found to rely heavilyupon heterotrophical ly-produced carbon inthe fomi of bacteria associated withdetritus (Provasoli et al. 1959; Brownand Sibert 1977; Sibert et al. 1977b;Kieper 1978; Vanden Berghe and Berymans1981 amony inany). Considerable speciesspecificvari abi 1 i ty in food preferencesmay exist, possibly reflecting divergentfunctional (i e. , mandible) morphologyand behavior (Marcotte 1977 and pers.coam,; Vanden Berghe and Bergmans 1981).This characterization as specialists,in terms of nutritional preferences andrequirements and the ability to utilizespecific foods, may explain the often extremefluctuations in epi benthic zoopl anktonassemblaye structure observed in verydynamic estuaries such as the ColumbiaRiver (Houghton et al. 1980). Some prominenttaxa, particularly Eurytemora atfin-- is, can effectively feed on both detritusand phytoplankton, and it has also beensuggested further that algal cells may actually contribute some trace metabolitenecessary tor normal egy production(Heinle et al. 1977). The presence ofprotozoa in association with the detritusmay also form a critical link between thedetrital POC and assimi 1 ation pathways ofepibenthic copepods. Mysids such asNeomysis mercedis may, in addition tobeing d e m e s and phytoplanktongrazers, be carnivores. A1 though theyare reported to consume primarily diatomsin the Sacramento-San Joaqui n estuary(Kost and Knight 19751, Houyhton et al.(1980) illustrated that N. mercedis inthe Columbia River estuary f e v t u n -istical ly upon meiofauna and zooplankton(cladocerans, cyclopoid, harpacticoid,and cal anoid Copepods ; roti fers) whichwere numerical 1 y prominent within theepibenthic region. Thi s feeding mode wasalso verified by ~iegfried and Kopache(1980), who found that, althouyh not aparticularly active predator, N. mercedisi n the Sacra~r~ento Ki ver estuary derived>80X of its energy via carnivory onroti fers and copepods ; di rect herbivoryappeared, in fact, to be of importanceonly during the spring diatom bloom.Wilson (1951) described N. rnercedis inthe Nicomekl and serpentine Rivers Estuariesas feediny on both vl ant (diatoms,dinoflagellates, blue-green alyae, vascularplant detritus) and animal matter(copepods and mysids), Johnson (1981)also describes the trophic role of N.mercedis in t3ri tish Col urnbia eStuari6?channelhabi tats.Estuarine pel ayic zooplankton andneuston, ~erhaps ref 1 ect i ny the lowerternporal and spatial diversity of avai 1-able food resources in the water columnas compared to bentnic and epibenthicenvirons, i 1 lustrate more 1 imited feedingstrateg ies. Most are suspension feeders(Davis 1949; Poulet 1973;Kichman et al.1977; Lonsdale et al. 1979), althoughsome omnivorous and carnivorous taxa arealso prominent (Anraku and Omori 1963;Gaul d 1966; Mu1 len 197 7) . In the case ofthe Pacific Northwest estuaries, vredomi -nant zoopl ankters incl ude both herbivores(i e., Eurytemora spp., Pseudocalanusspp., and Corycaeus angl icus) and omnivores(Acartia spp. ), which thernsel vesmav be trovhically linked (Hodqkin andNext to the avian assemblages, demersalfishes illustrate the rr~ost diversespectrum of Food web linkages and trophiclevels in the habitat. This includes afew primary consumers (i.e.,comnion carpfeed considerably upon algae and otherplant material as we11 as detritus;Wydoski and Whitney 1979), many secondaryconsumers and some species (i.e.,doyfish,linycod) which could be consideredtertiary COnSUmerS although they are, inturn, susceptible to predation by othertertiary Consumers such as marine mammal sand, of course, man. Some species may,throughout the ontoyenet ic chanyes in

feeding behavior, encompass several troph- greater selectivity upon predominantly feiclevels and prey assemblages; white male A. californiensis and both sexes ofsturgeon, for instance, are reported to -- A. clGsi. Considering the overall dietsconsume everythiny from epibenthic zoo- of these three pl anktivores, adult femal eplankton as juveniles to salnion and house - A. californiensis composed 34.1% of thecats (a prime illustration of interhabi- total number and 53.6% of the -A. cal i forn-tat 1 inkages!) as adults. Ainong the iensis fraction.reprcserltative species (Tab1 e 6.1)facul tati ve epi benthic benthivores (17species; 40%) and facultative epibenthic The five species of juvenile salmon,pl anktivores (12; 28%) predominate, fol - whose food habits have been studied extenlowedby obligate epibenthic benthivores sively (summarized in part by Levy and(5: 12%) , obligate epibenthic plankti- Levings 1978; Levy et al. 1979; Northcotevores (4; 9%), omnivores and parasites et al. 1979; Levy and Northcote 1981;(2; 5%), and facultative meiobenthic Durkin 1982; Healey 1982; and Simenstadbenthivoes (1; 2%). This composition et dl. 1982b), also illustrate the variedchanyes, of course, with seasonal changes prey resource uti 1 i zation patterns whichin assembl age structure and with growth have evolved among congeneric taxa, Juveanddevelopment of resident species.nile pink salmon occupy shallow sublittora1habitats for very short periods (days)Reflecting the re1 ative simp1 icity before moving rapidly to pelagic channelof their prey resources, pelayic fishes or neritic habitats, feeding predominantalsoi 11 ustrate less diverse feeding ly upon cal anoid copepods and larvaceans.strateyies tnan the deinersal assemblage. Contrastingly, juvenile chum salmon typi-Of the representative species (Tabl e G.2), cal ly occupy shal low subl i ttoral habiallbut two are primarily planktivorous, tats, es(~eciall1 sand-eel grass, forwith onlj cutthroat trout and Dolly Var- several weeks feeding upon epibenthicden exploiting other fishes. Two thirds zooplankton, particularly harpacticoid(24) of the species are obligate pelagic copepods and gammarid emphipods; uponpl anktivores , i ncludiny two-thi rds of growing to 50-60 mm FL, tne juveni 1 ethese (16) which occur only as pelagic chums also shift to pelagic channel orlarvae. Four each (11%) are facultative neritic habitats where they feed uponpelayic pl anktivores or epibenthic pl ank- calanoid copepods, decapod 1 arvae, andtivores and two each (6%) are obliyate 1 arvaceans. Juvenile coho salmon feedepi benthic pl anktivores or facultative principally upon gamrnarid amphi pods durpelagicpi scivores. While the dominant i ng their relatively brief occupation ofzooplankton taxa comprise the principal shallow subl i ttoral habitats, particularpreyresources of the planktivores, con- ly exposed yravel beaches, and upon decaslderablesize- or taxa-selective preda- pod larvae and euphausiids after movingtion characterizes individual species and into eplayic or neritic habitats. Sur-1 i fe hi story stayes. prisingly little is known about the estuarineforaying behavior or prey composi-This was effectively illustrated by tion of juvenile sockeye salmon due toJohnson's (1981) detailed examination of their rapid emmi yration throuyh estuarinethe diets of three prominent pel agic and nearshore marine habitats. Juvenileplankti vores in Yaquina Bay-- juvenil e shrimp and euphausi ids have been reportednorthern anchovy, topsinel t, and surf as the prey of juvenile sockeye miyratinysmelt--relative to predation rates upon out of Puget Sound. Small juvenile chi-Acartia californiensis. When foraying in nook salmon tend to utilize shallow subthewater column, juvenile anchovy were littoral, salt marsh, or mudflat habitatshighly selective toward the larger female early in their estuarine residence, and- A. cali forniensi s and A. clausi , Eury- feed upon yarnmarid emphi pods, cumaceans,ternora affinis, and the clad-n podon; and emergent and drift insects. Upon growsurfsmemectedsimilar feeding =- iny larger or upon enteriny the estuarytivity while topsmelt reflected even at a 1 arger size as sm01tS (60-70 mm EL),106

they move into pelayic or neritic habitatsbut continue to feed upon drift insects,as well as decapod and tish larvae.Extremely Selective forayiny is also oftenevident within these broad prey categories.For example, in shallow sublittoralhabitats juvenile chum salmon tendto feed on a narrow spectrum of harpacticoids>75 pm in length and, at least witninPuyet Sound, particularly the speciesHarpacticus uni remi s. When in the pelayichabitats, they appear to select re1 a-tively rare but very large (>2 mlil inlength) calanoid copepods such as Calanusspp. and Epilabidocera spp. instead ofother, more numerousbut small er cal anoid(i e., ~eudoca'lanus sp.) and cyclopoid(i.e. , Corycaeus spp. ) copepods (Simenstadet al. 1980). Several of the otherspecies of juvenile salmon show similarlyselective foraying(Table 9.1).in estuari ne~hdn~el SFood habits data addressin9 the region'sbird fauna which specifically oc-Curs In estuarine channel habitats is almostnon-existent and essenti af ly l imi tedto semi -qua1 itative data from GraysHarbor (Salo 1975; Smith and Mudd 1976a).Food web re1 atjonshi ps of more marine/coastal bird dsselllblayes have been Summarizedby Sirnenstad et al. (197%) intheir synthesis of nearshore and neritichabitats of the northern Puyet Sound andStrait of Juan de Fuca ecosystem. Of thefour syntopic species of marine divingbirds examined by Scott (1973) in the vicinityof Yaquina Uay, two (common murreand Brandt 's cormorant) may have acqui redTable 9.1. Principal preferred prey taxa of juvenile salmon in Pacific Northwest estuariesbased on 1 i terature and other stomach contents data sources.JuvenileSizesalmonclassspecies (mm,FL) Preferred prey taxaOncorhynchus gorbuschaPink salmon0. keta, chum salmon - -40-60 Calanoid copepods, Pseudocalanus spp.Larvaceans Oi kopleura sp.35-55 Harpacticoid copepods Harpacticus uni remi sGamri~arid amphipod Corophium syp.Cumacean Cumel 1 a vul garis- 0. kisutch, coho salmon >55 Calanoid copepods Galanus Spp., EyilabidoceraGammardi amphi pods Eoyanln~arus spp.!orophi urn spp.Ca anoid copepods Eurytemora sp. , Cal anus sp.-- U. nerka, sockeye salmon 45-91 Adult insects Dipterans, Ho~nopteraEuphausiids Thysanoessa spp.- 0. tshawytscha, chinook 35-75 Chironomid larvae and pupaesalmon Gammarid amphi pods Eoyammarus spp. ,Corophiurn spp., Aniso amnarus spp.~umaceans -cumel la V*Isopods Gnorimosphaeromd oregonens j s> 75 Adult insects Diptera, Homoptera

a portion of their diet from within estuarinehabitats; coincidental ly, it wasthese same two species which Wiens andScott (1975) calculated to cycle theyreatest annual flow of tropnic eneryy.The four representat i ve bi rd assemblayesillustrate a dfverse spectrum offeeding types (Tab1 e 7.1). Shal low-probinyand surface searching-shorebi rds, asthe assemblage irnpl ies, are prfncipal ly(71%) obligate benthivores which teed onbenthic intauna and epibenthic zooplanktonalong the channel margin; toe otherspecies are on~nivores whose diet includesV~SCUI ar plant matter (including seeds)froill adjacent marsh or terrestrial habitats.Waders are either functional benthivoreswho prey on similar, though somewhatdeeper, benthic organisms as thefirst assemblage or dre carnivorous (obl i-gate or functional piscivores) on fishesand motile epi faunal invertebrates whichventure into shal low sub1 i ttoral areas ofttie habitat. Surface and diviny waterbirds,the 1 argest assemblage, includesseven feediny types, over a third ofwhich are functional benthivores. Ubligateand functional piscivores and omnivoreseach conrprise 19% of the total numberof species in the assemblage althouyhomnivores usually utilize estuarine channelsonly for roostiny, Obligate herbivoresand obl iyate and function1 pl ankt i-vores were represented by one specieseach. Amony the nine representativederial -search i ny bl rds, two-thi rds arehiyher level carnivores, either piscivoresor avivores, while two are obliyateinsectivores and one is an obligateylanktivore.Recent studies In the Columbia Riverand adjacent estuaries have provided thefirst datd directly focused upon estuarineutil ization by aquatic (Dunn et a1 .1981) and marine mammals (Howerton et al.1980; Beach et al. 1981) which includeschannel -specific food habl ts information;previous i nvesti yations tended to beeither semi -quanti tat1 ve and not channelspecific(Smith and Mudd 1976b) or wereoriented toward marine and neritic habitats(summarized by Simenstad et al,1979a and subsequently by Everitt andJeffries 1973; Everitt et al. 1980).Among the five representative terrestrialand aquatic mammals (Table 8.1),three are obligate herbivores whichobtain their plant foods in adjacentterrestrial and wetland habitats whiletwo are epibenthic carnivores whichventure into channel habitats to feed.Beaver feeding activity in the ColumbiaRiver occurred principal ly in Si tkaspruce habitat during a1 1 seasons exceptwinter, when activity in the Sitka wil lowhabitat was higher (Dunn et dl. 1981).Muskrat and nutria, on the other hand,forage principal ly in high marsh habitats(Section 8.2), where muskrat preferentiallyeat water parsnip (- suave), Lyngbye'ssedge (Carex lynqbeyinnd softstgnbul r?lSh (Sci rpus val idus) ; and nutriafeed on a broader spectrum of plants, in-sedge, tufteds itosa),7h water parsnip, and s o m mbuirush (Howerton et al, 1980; Dunn etal. 1981). While muskrat illustrated nomajor seasonal variation in their foragingbehavior, nutria feeding (no. feedingsites hectare-1) appeared to reach amaximum in the fall and minimum in thesulnner: The reed canarygrasslca ttailhabitat was the most common foraging habitatin the spring and summer, Lyngby'ssedye/horsetai 1 in the fa1 1, and colonizingsoft-stem bulrush during the winter.Raccoon, the only truly terrestrial mammalutilizing estuarine channels forfood resources, prey principal ly uponmolluscs (e.g., clams such as Corbiculamani lensis and Anodonta sp. ), moti leepibenthic crustaceans (e.y., crayfishand crabs), and fishes (e.g., eulachon,sculpins such as Cottus sp., carp, andstarry flounder) with secondary inputfrom birds (particularly waterfowl ) andpl ant (rosaceae) seeds and frults (Dunnet al. 1981). River otter in the ColumbiaRiver estuary generally overlappedwith raccoon in their prey cornposition(principally crayfish, carp, Cottus sp.,scul pins, and starry flounder), ected

a diet generally si:nil ar to that reportedby Hi rscni (1978).A1 1 four represer~tati ve marine mammalsare facultative carnivores, threefocusiny tnei r toraging principal ly uponpelagic prey assemblages and one on epibenthicassemblages (Table 8.1). Northernsea lions follow baitfish (e.y.,euldcnon) and salmon (e.~., spriny chinook)into estuaries such as the Columbia(Beach et al. 1981), feeding principallyat night and probably a1 so corisu~ning otherschooling or large pelagic fishes inchannel habitats (Simenstad et a1 . 1979a).As with the northern sea lion, noquantitative data on estuarine prey ofCalifornia sea lions is available forthis region, but it would be reasonableto assuae thdt other pelagic schoolingfishes (e.y., Pacific herring, northernanchovy, Pacific sand lance) and largedemersal species (Pacific tomcod, starryflounder) a1 so constitute potential preyin estuarine channels.In addition to the focused, intensiveforaying on eulachon in the ColumbiaRiver, harbor seals there and in otherestuaries of the region prey upon otherpel ayic school iny and dernersal tish assemulages and moti 1 e nlacroi nvertebrates ofchannel and l i ttoral flat habi tats(Scheffer and Sperry 1931; Scheffer andSlipp 1944; Fisher 1952; Simenstad et at.1979a; brown 1980; Everitt et al. 1980;Beach et al. 1981; Sow1 by 1981). Accordinyly,principal prey species will includeeul achon, northern anchovy, whitebaitsmelt, Pacific sand lance, lonyfinsmelt, and Pacific herring amony theschooliny pelayic fishes; Pacific torncod,Pacific staghorn scul pin, snake prickleback,Enyl ish sole, starry flounder,shiner perch, 1 inycod, and bay yoby amonythe demersal fish assemblage ; and cranyonidshrimp and Dungeness crab among themoti 1 e macroi nvertebrates. Other preywhicn have been reported as prominent inharbor seal diet spectra, includingPaci fit hake (Merl uccius productus), walleyepol lock (Theragra chalcogramma) ,Pacific cod (Gadus n~acrocephalus) , variousspecies of rockfish (Sebastes spp.),rex (Glyi~tocephalus - zachmpetral e(Eopsetta jordani), and Dover soles(Microstomus pacificus), are probablycaptured in non-estuarne habitats or inthe outer liarg gin ot the estuaries' euhalineregions. Considerable inter-estuaryand seasonal variation in diet coa~ositionalso persists. Beach et al.'s(1981) analysis of harbor seal scat collectedbetween June 1980 and April 1981in the three major coastal estuaries ofWashington indicates significant rank importance(based on frequency of occurrence)differences. For example, Paci f iccod (20X), unidenti tied crustaceans (la%,probably crangonid shrimp and Dunyenesscrab), Pacific stayhorn sculpin (16%).lonyfin smelt (15%), northern anchovy(14%), eulachon (13%), and snake prickleback(lC)%) were important in the ColumbiaHi ver estuary; northern anchovy (21%),Pacific stayhorn scul~in (19X), unidentifiedcrustaceans (15%), shiner perch(13%), Dunyeness crab (12%), and starryflounder (1UX) domindted the prey spectrumin Willapa Bay; and northern anchovy(49%), Pacific staghorn sculpin (34%),English sole (23%), Pacific tomcod (17%),Dunyeness crab (15%), and starry flounder(11%) predominated in Grays Harbor.Unequal monthly and total sample sizesand the inherent biases of frequency ofoccurrence data should be taken intoaccount in evaluating these differencesbut the structural variability, as wellas the commonality, in food web linkayesbetween harbor seals and the variablesecondary consumer levels in the threeestuaries is apparent.Seasonal diet variability is alsoobvious. 8each et al. (1981) also describedseal forayiny in the ColumbiaRiver estuary as shifting markedly fromeulachon in the winter, to lampreys(class Aynatha, principally Lampetraspp.) in early spring, moti le macrolnvertebrates(crustacea) in late spriny, anda diverse, opportunistic selection offishes trom summer to winter months.Seasonal shifts in Willapa Bay harborseal diets were re1 atively di tferent,from crustaceans in winter, to northernanchovy from spriny through late summer,and a broader spectrum of tish species(led by Pacific stagnorn scul~in and

northern ancnovy) trom sumer throughfa1 1. Likewise, Grays Harbor seals maintaineda relatively different seasonaldlct pattern: frm Pacfic staghornsculplns, pleuronectids, Pacific romcod,and crangonrd shrimp in the winter, to adiverse array of tisrl anu Uunyeness crabtn the summer, to an emphasis upon northernancnovy In late sunmer, to Pacificstaynorn sculptn and Enylisti soie in thefall.In addttion to these natural preyitems, harbor seals, in conjunction withCalltornfa sea lfons, are also consideredto ue the principal cause of nlcsrfne mammaldarndye to fishing year but appear tobe ~lntost ~*o\ety responsible for damagetrt nc?t-~bpt~red Zfsh, which accounts toraa high as 7% of the sdmpled catch (Beachct 41. 1PliS1).Rltnuugh tncre are not data ontl,+rtrasr scat diet specific to estuarinechnfit~thl hdbttat~ wl thln the Strsi ts of,lurli? clc lt~fa irnd tinuryfe and lbuyet Sound,Interrtnatdon documented traca this region(St.ttc?ltcr atra Spcrry 19331; Fisher 1952;Catdmb~kidtb et al. 1978; Sirnenstad et61. tQ79a; Everltl ct &I. 1980) indicatesctst~slclerable overlap in prey taxa, indicatlng that tt~tuarine channel tauna conktttute& wjor element of RarbOr sealFcrurl rurource tn fnland waters. anlytrbytt\et~tb~+y ditta fs available on tneirtoatf RbOlts and llttle originates tronrtnts rciyion; prey am assumed to beyr-tnclpal ly dmcrsill fish, and pelagicft$ti and CP~R~~OCJOCIS (Stmenstad et at,191Ya; Antunel 1s snd Flscus 1980; Everittet a!. l!&B.l).frrter~rttaion ot these tood web relatronbnrpsr~suits in a coml~osite food webtor P$EUI~~IICP channel comun t t ies (fig.G.1) which is at least quatftativelyartentea more toward aetrltus util lzalionand heter~tr0yfitt pr~duction than towardpelaylc auCutrayntr production. If Stand-Iny stock of detfltlvares and tneir yredatarsr?; lndiedtlve, the food webs arequa1 't tatively dmrnatett by detrital car-%ran, As idenertrea ~?y de Sylva (1975).Udm! and Maa~ld (197s). and Northcote etat. (23731, insst Gtstuartne rood webs fallinto two cateyorles: 1) relativelyclear, deep systerns where organic caraonis derived prlmarl ly frorrl phytoplanhtonproduction, and 2) compdrdtlvely turbld,snal low estuaries wnere the cdrbonoriginates trom a cornbinatton ofmacrophyf lc production (both exoyenOuSand endogenous), wn iCh I s degrdded todetritus and utlllred by mlcroftord, anaperipnyte productlon. Very tew estudrtesin the Paclfic Northwest fall Into tnefirst cateyory, especial ly tf we lncludethose estuarres which, althougn seldomturbid, may nave tood webs based upondynamic, short-tenn recycl 1 ny ot endoyenouscarbon exuded ay any 1 ospernts, Inac roalgae,and eplynytes (Wlssrl~ar an0 Slfnenstad,Fish. Kes. Inst., Uniw. Wash.,unpubl. aata; see Sectlon 4.1). Thus,direct (pelagic) autotrovnic productlunIs only maryinal\y supportive of estuarinetood WDS In tne reylon dnd is yrnerallyrestricted to tne larye codstalestuarle~ wnere treshwa ter dnd estur lnephytoplanktrrs are entrained in a conf1 ned euvhot I c zone.A~nony these yeneral ized food wea1 inkayes $re several dl st 1 nct modules(Palfle 1980) which typi ty estuar~ne cndnnelco~rmunities, not only in structurebut ofteri In cotirnon consunrer taxa. 'fhrsoorrest, least-conlpartmented food web(it is still a "web" due to conSlderabiepredator-prey interaction within dcoqartm@nt such as tot! benthic lntduna)is that Northcote et a]. (1979) descrlbeaBS :detrft~s~benthos~benttto~ndyous f t sneswhen tertiary Consumers included, thearchetyptcal food webs in this cdrrgurywould rnclude both "cfetritus:benthrc1nfauna:obl iyate ~entnlvore: tunctrondepibentnic cdrnivore" iirodules ds wel 1 as"artri tus :@pibenthic zoop t ankton: tuneti~naleyibenthlc plarrkt~vores :tunctlont~1eprarntnlc carnivore" modules such as:More con~ylexr ty is evident in detrl tusbased,eyibenthic ntodules which involve

PRODUCERFig. 9.1. Representative food web of estuarine channel habitats of the Pacific Northwest;sizes of linkage arrows illustrate relative biomass transfer.meiofauna carnivores such as Crangon spp.or benthic carnivores such as Cancerspp., resul tiny in "detritus :detritivorouseyi benthic zooplankton: benthiclepi benthiccarnivore (2') :facultative epibenthiccarnivore (3")" modules such as:Planktonic food webs are characteristicallyshorter, as represented by thephytopl ankton: herbivorous pelagic zooplankton:obl igate planktivore: obl igatepiscivore module, a1 though they can becomplicated by the inclusion of carnivorouszooplankton such as Acartia spp.,where:The ul tirnate compl exi ty is represented bymodules including species ~hich are eitherextre~liely plastic (facul tative) in thefeediny behavior or incorporate or growthrough several feeding strategies overthe period of residence in the estuary.This is particularly evident in the caseof juvenile salmonids, vrhich utilize bothendogenous and exogenous (to the habitatand, often the estuary) detritivores andherbivores. The resulting modules can beambi yuously described as detri tus/phytoplankton:detritivorous epibenthic zooplankton/herbivorous pel ay ic zoopl ankton:epibenthiccarnivore: facul tative epibenthiclpelagicp1anktivore:obligatepiscivore such as shown on the fol lollringpage. Of course, this complexity seldomexists to this extent within any channelclass, order, or configuration, or anysize class of consumer (e.g., juvenilesalmonid) at any one time, but variesuniquely as a function of all these variables.

Classically, the diversity (i.e.,nul-iber of connecttons ar "connectence" )and strength of these interactions havebeen correlated wllth the stability (i.e.,its inherent susceptlbf 1 t ty to collapse toa JJfferent, usually less dlverse structurewhen perturbed by removal of 1 f nkagesor nodes); this poses the question ofdhekher food webs are "structured" or"unstructured" (MacArthur 1955; Watt 1964;Paine 1966, 1969; Sardner and Ashby 1370;lsadcr; 1972, 1973; May 1972, 1973; DeAncjelis 1975), Thc imp1 icatfons of mutatirricrrlalfonships have also been recentlyitlclrrpor~ted into these models (Vance19183. Onfartunately, the functionalr.;rilience of these mdules, thelr linkages,and thelr dependence upon externalevents; has seldom been tnvesttgated frmthe s tat~dpoint af the processes genera tinytilei r structure and, until that resolut tonuf rvrearch is appl led to estuarine chantrrleun~rtuni tics, the ques tlon of food webstdbi l "ry wJll reinah unresolved,We can,hoii~ever, set ec t f vlely examine ercempl ars ofpratnJnent predator-prey or competitionintersctfons far clues to the strength ofI inkages within representative mcxiules or00 the potential stabi? ity of the slrnplerisvdul es & &I&,41.2 ROLES OF PREDATION RNO COMPETI-IIW lNTEri4CTlONS If4 SPRUCTURIK COM-MVOUNITIES AhtD PO00 MfDSThere are, among the modules dencrtbedIn the prev fous section, i 1 lustratjons of strong predator-prey and cwnpetitlvninteractlcrns wherein the distrlbutqonand slbundance of estuarine channel organlsrzlr,and thus the structure of thecornauni ty, a* canetagant upon the presenceand myna tude of these 1 inkages.A1 though fw of these examples originatefratn Pacific Horthwes t estuaries, they aresufficiently close analogues that reasanableinferences to the region's estuarinechannel cawunities might be inade.One of the strongest linkages suggestedis that between the cdlanoid &- tia spp. which could represent an importantpredator upon the larvae of thedominant estuarine calanoid in the region,and Rippingale'sof Cronin et al.and Jeffrles (1967) accounts ofzooplankton in North Aerican estuariesindicated that Acartia, by its carnivoryupon crf tfcal l h i s t o r ~ stages of thecs tuari es' Eur te~nora populations, mayprevent r i g a 4 ~ r e c r utment i to theadult population, Cocnparable AcartiaJElr temora data sets also exist m a -&a Bay (Frolander et al. 1913). theColumbia River estuary (Haertel and 0s terbery1967). Netarts Bay (Ziminerman 1972),and Grays Harbor (Simenstad and Eggers1981). Further testing and verificationof this hypothesis mst depend upon furtherdetailed analysis of these datasets.The potential for predation structuringof epiknthic harpacticoid copepaddssefnblages 4n shal low sub1 i ttoral habttatsof Hood Canal by juvenile chum salmonwas suggested by Simenstad et al. (1980)and Sitenstad and Salo (1982). Given theintensive, selective foraging pressurethat juveni Ie saltwnids exert upon epibenthicharpacticoid copepod (e.g Nargamnaridanphlpod 'it?=,M A j * and cumacean (e.g.. Cumella)& t is highly probable that p-dforaging upon these epibenthic preyresources by high deqsi ties of juvenilesaltnon could resul t in dratna tic res tructurlnyof that assetnblage. This is evenmore probable gfven the high density,pulse releases of juvenile salmon fromhatcheries which may result in mf 11 ions offish entering estuaries at one time.A1 though there has been no comprehensive,estuary-ride exdrnfnatian of such arelatianship, the same situation may existin the pelagic environs uf those estuarieswhich experience high densities of larval

and juvenile plankti vorous fish. YaquinaBay, the Columbia River estuary, and GraysHarbor have we1 1-documented concentrationsof Paci f ic herring, northern anchovy, andsmelts (particularly surf and longfin)which are both temporally and spatiallyabundant duri ng certain seasons (see Section6.2). But Johnson's (1981) analysisof the Acartia cal i forniensis populationin Yaquina Bay (see Section 5.4) providesample 'evi den& that such selecti ve predationcan effectively control abundancecycles, and ul tiinately production, of theprorilinent members of these zoopl anktonassemblages. Under such intense andselective foraging pressure on pelagiczooplankton, predominantly these calanoidcopepod taxa, these obl igate pl ankt ivoresmay we1 1 structure the composition, diversity, and standing stock of the estuarinechannel zooplankton assemblage.Si tts and Knight (1979) and others(C. Simenstad, Fish. Res. Inst., Univ,Wash., unpubl. data) have produced evidencethat the crangonid shrimp Cran onfranci scorum of ten feeds extensive I-- y uponthe mysid Neoniysis mercedis. Si tts andKnight in fact, estimated that C. franciscoruniremoved between 0.1% and 5 . 0 m e- N. mercedis biomass daily from the Sacramento-SanJoaquin River estuary, and that,by preying selectively upon intermediatesized (4-7 mm) mysids, the shrimp aresignificantly affecting the mysid populationstructure. The persistence of such aCrangon-Neomysi s interact ion in the Paci f-ic Northwest, particularly in the largecoastal estuaries which maintain largepopulations of both taxa, is highly probableand further il lustrates the importanceof the detritus-based module involving thee ~ benthic i zoopl ankton prey of inysids (l.iercedi s) and ' shrimp (c.- franci scorum~,and the ~rominent predators on the shrimp(starry 'flounder and harbor seal). Therelative importance of this particularmodule may be evaluated in final synthesisof the CREDDP studies (Col. Riv. Est.Study Team, pers. comm.), which includedquatti tative assessment of these taxa inthe Colurnbia River estuary in 1980-1981.9.3 ESTUARINE CHANNELS AS CRITICAL REPRO-DUCT1 VE, NURSERY , FORAGING, AND REFU-GIA HABITATSEstabl ishment of uti 1 i zation patternsand food web \nodules involving estuarineorganisms carries iinp1 ici t assumptions ofdependence upon these re1 a tionships mostof which, however, are co~npl etely unverifiable.Uhether the loss or major disruptionof a food web linkage or microhabitatwould actually result in the subsequentdecl ine in the population remains conjectureunless control 1 ed rnanipul ationexperiinents can he conducted. Out, unlikethose which have been successfully conductedin marine rocky 1 i ttoral (see Paine1977, a~nany rnany) and shal low sub1 i ttoralsand- or mudfl at habi tats (Vi rnstein 1977;and Aoodin 1951; among not so many; hutsee Hurlberg and 01 iver 1980 for discussionof interpretive 1 irni tations), effec-tive manipulations within the dynamicestuarine channel habi tats have seldombeen attempted and would be even inoredifficult to interpret due to extremevariation in uncontrollable physiochernicalconditions. The fol lowi ng il lustrationsof potentially "critical" habitat associationsare, therefore, only descriptivehypotheses which relnai n to be effectivelytested.Compared wi ttl other habitats, estuarinechannels appear to be limited inproviding optimum condi ti ons for reproductionof most fauna. Except in the case ofblind (e.g., tidal) channels, high watervelocities and uns tab1 e bottom sedimentsin most channel habitats inhibit manyinvertebrates and vertebrates from establishingnesting sites; even the suitabilityof the tidal channels is often limitedby tidal dewatering, Fauna which dospawn in channels typi cal ly depos it adhesiveeggs (gastropods, 1 i ngcod) , burytheir eggs (salmon), or carry and broodthe eggs and 1 arvae/ juveni les (gammari damphipods, i .e., Eogammarus spp. ;Dungeness crab). But, except for thespawniny immigration of salmon (typicallychum and pink salmon) into the channelsof estuaries' upper reaches, most repraductiveactivities are confined to residentfauna which undergo their entire life

cycle within the estuary. Many estuarineresidents, however, mi grate from channelto other habitats to reproduce. Estuarinebirds, of course, are the extremecase, as none actually nest within thehabitat. But resident fishes such assturgeons, smet ts, gobies, stickelbacks,and many sculplns move to either channelboundaries or other esturf ne habitats(e.y., shat low sublittoral or littoralsand- or mudflats; saltmarshes) to spawn.whether from resident or exoyenouspopulations, both f nvertebrate and vertebratelarvae and juveni 1 es can residewithin estuarine channels for extendedperiods of time, essentially utilf zingthe habitat as a "nursery" until settl inyout into benthic, epibenthfc, or demersalassemblages ar moving out of the habitat.The net outlfow circulation pattern ofthe estuaries, however, represents a majorinhibitor to prolonged entrainment ofyldnktonic larvae. Assuming neutral buoyancyand passive behavior, the minimumrate of reproduction reqtlired for an endm1c zooplankton popul at Ion to maintainitself in an estuary is detern~ined by therate ot circulation, such that reproductionmust be higher than the tidal exchangetoss rate (Ketchurn 1951, 1954).But the organisms' behavior is not passiveand yartjcular li te history patternsand behaviors of such organisms haveevolved to oytimfze thelr estuarine residencetfrne. Carriker (1951). Bousfield( 1955). Pearcy (1962)" Wood and Haryis(1971), Graham (1972), de Woiff (1974),Sandlfer (1915), Wheeler and Epifanlo(1978). Cronin and Forward (1979), andCronin (1982) have a1 1 described behavioralretention mechani smS exhibited by1 arvae in two-l ayered estuaries havjnynet landward flow along the bottom duringperiods when larvae arc? abundant, Theirstudles i 1 lustrated that larvae can prolongtheir resjdence in the estuary byact1 vely nrigrating into the landward-f lowingsurtace water on flood Cfdes. Slmilarretention mechani sins have a1 so been postulatedto account for the maintenance ofresident mop1 ankton (e.9.. 1populations in estuarjes (KO ,Hurl ber t 1957; Wooldridge and Erasmus1980). Carri ker (1959) , Sandifer (1975),and Johnson and Gonor ( 1982) , however,have i 1 lustrated situations where s mestuarine larvae are flushed out of theestuary of origin, only to be transportedback into other, adjacent estuaries aslater larvae, post-larvae, or juveniles*Johnson and Gonor (1982), in fact, estimatedthat 88% of the total abundance ofCall ianassa cal iforniensis stage I zoeawere carried out of the Salmon River estuaryon the ebbing tide; this would resultin a "leap-frog" transport and metamorphosisof larvae in and out of estuariesalong the coast until they settled out inthe benthic form. Johnson and Gonor (1982)suggested that the concentration of Call i --- anassa larvae in the coastal n m cwaters and successful recruitment tocoastal estuaries was enhanced by thealternation of active upwelling and relaxationperiods which Huyer (1976) describedoff Oregon. Thus, the extent and importanceof estuarine retention of larvae maydepend upon both the position of the repraducingpopulation, since maximum retentionwill occur with populations in theupper reaches of the estuary (Dayton andOliver 1980), as well as the evolved behavforal repertalre and seasonal periodic-Ity of the reproductive and early lifehistory events.Pearcy and Myers (1974) provide oneof the few comprehensive assessments ofthe value of a Pacific Northwest estuaryas a nursery habitat for larval fishes,excludiny McHuyh's (19b7) suggestion thatPactffc coast estuaries are less importantthan eastern seaboard estuaries.They established that, indeed, larvae ofmost species were Inore common off shorethan wlthin the estuary and that Pacificherring larvae were the only commerciallyimportantspecies to utilize the estuaryas a nursery habitat. Other, lessnetarious species whlch were also identifiedto utilize Yaqulna Bay were baygoby, prickly sculpfn, buffalo sculpin,and Pacific staynorn sculpin (see Table6.21; other studies also suqqested thatposiiarval and juvenile embiotocids (P.furcatus, R, vacca, and E, IateraliT)no-G$ pr%mini(8eardsl@ 1969; WaresIYtlf. Later studies of the zoo- and ichthyoplanktonof the Columbia River and

Grays Harbor estuaries suggest that larvaland juvenile northern anchovy, surfand longfin smelt, and eulachon shouldalso be considered as nursery residentsin the coastal estuaries (see Sections6.2.1-6.2.3.).Although their larvae are not oftendocumented as abundant components of theichthyopl ankton, juvenile pleuronectids(prominently starry flounder, Englishsole, and speckled and Pacific sanddab)are abundant in demersal f i sh assemblages,particularly those which occupy shallowsubl i ttoral regions of estuarine channeland adjacent tideflat habitats (Westrheim1955; Beardsley 1969; 01sen and Pratt1973; as well as those cited in Section6.1). These species often i 1 lustrateincreasingly deeper depth di stri bu tionsrelative to increasing fish size, suchthat they appear to move off the tideflatsand further into the channels as they growlarger. This depth-size relationship hasnot been well-documented, nor have thecausal mechani s~ns been evaluated, a1 thoughboth predator avoidance and foraying onoptimal prey resources could explain thistransition.Juvenile salmonids illustrate one ofthe better example of active retention inestuarine channels over a critical periodin their early life history. The fivespecies show varying durations of estuarineresidence (Table 6.3), with markedintraspecific variation resulting fromrespectively variable times and sizes atentry into the estuary. Within the estuaryare a diverse array of prey resources,often in extremely high density(e.9, , harpacticoid copepods, Coro hiumamphi pods, chi ronomi d 1 arvae, decapod -7 anfish larvae), which allow the juvenilesalmon to sustain high growth rates (ashigh as 6% body weight per day) whileoccupying a relative refugia from predation(Simenstad et al. 1982b); whetherthrough schooling in shal low subl i ttoral ,eelgrass habitats (i e., juvenile chumsalmon) or turbid pelagic waters (i.e.,chinook smolts), these systems may benarrowi ng the "wi ndow of vul nerabi 1 i ty"to predation outside the estuary by "growingout" of it while in the estudry.This relationship between estuarineresidence time and foraging success, andthe implications to the total marinesurvival rate, suggests that the distributionand dbundancu of the principalpreferred prey (Table 9.1) ultimatelydetermine the production of the salmonpopulations migrating through the system(Northcote et al. 1979; Simenstad andSal o 1982; Simenstad et a1 . 1982a, b).9.4 INTEKKELATIONSHIPS AMONG ESTUARINECHANNEL HABlTATS AND RIVEKINE, WET-LAND, OCEANIC, AND OTHER ESTUARINEHABITATSFood web and other ecological interactionsamong channel and other estuarinehabitats as well as with habitats outsidethe estuary are manifold. They rangefroin simple transport of pelagic phytoplanktonand zooplankton into and out ofthe channel community from and to riverineand oceanic sources, to the complexexchange and entrainment of exogenousdetritus. These, like the transport oflarval fish and invertebrates into thehabitat, are relatively passive actionswhich result from physical (e.g., tidal)influences. Other transfers, such as themigrations of anadromous fishes and birds,can occur on a seasonal scale, whereasthe movement of fishes from the shallowsublittoral flat habitats into the channelhabitats with tidal dewatering occurapproximately every six hours, invol veactive movements of organisms but may beequally predictable.At the base of the estuarine channelfood web, detritus constitutes the mostcritical material originating from outsidethe community. Alteration of thedetritus resource--its supply, timing, orcharacter--to estuarine channels posesdirect impacts upon the structure andstanding stock of all consumer organismsin those food web modules based upondetritivores. Whether originating fromriverine sources completely outside theestuary (e.9.. DOC; Naiman and Sibert1978) or from within adjacent habitats(vascular sal tmarsh plants; Kistritz andYesaki 1979), the accumulation and retentionof detritus is dependent upon the

compl ex factors effecting ci rcul at ion andsal i nity intrusion. The endogenous sourcesof trophic energy, autotrophic producerssuch as phytoplankton and algae, donot, on the other hand, provide an equivalentproportion of the total carbon budgetcycling through the community.Primary consumers are typically endemic populations. Benthic 1 nf auna andsessi le epifauna are 0bvi0u~ly residentassemblayes but the organisms recruitinyto these populations oriyinate from parentassemblayes outside that particul arestuary, perhaps even from other, adjacentestuaries (see Section 9.3). Extremeexamples of primary consumers (orprey resources of secondary consumerssuch as juvenile salmonids) which origi -nate from outside the community are theterrestrial insects which are transportedinto the neuston assemblage from thewatershed upriver or are blown in frornwet1 and and up1 and habitats bordering theestuary.More motile secondary and tertiaryconsumers include progressively more non-endemi c popul ati ons, which either derivetheir recruitment from outside the community (e.g., Pacific herring, northernanchovy) or intermi ttently occupy thehabitat for important functions (e.g.,foraging by harbor seals; roosting by migratoryseabirds ). Accordingly , many ofthese immigrants are critical componentsof prominent food web modules and throughthese roles are largely responsible forthe structure of their prey assemblages.The community a1 so exports considerablebiomass, both passively through thenet flow out of the system, carrying varying proport ions of the pel agi c phytopl anktonand zooplankton to oceanic habitats,and actively through the emmigration ofsecondary and tertiary consumers. Theend result of the nursery process involvinglarval and juvenile fishes discussedearlier provides the best example of thisexport: almost a1 1 bai tfi sn--herring,smelts, anchovies, eul achon--whi ch residein estuarine channels during their early1 i fe hi story eventual ly mi grate out ofthe estuary after consuming a large portionof several year's pelagic zooplanktonproduction.

CHAPTER 10SUMMARY - THE ROLE OF CHANNEL HABITATS IN ESTUARINEECOSYSTEMS AND MANAGEMENT IMPLICATIONSIn essence, the role of channel habitatscan metaphorically be equated to thatof any 1 i vi ng organi sm' s circulatory systemin that transport of energy, nutrients,wastes, and the living products ofan estuarine ecosystem flow within thesepassages. Similarly, as the loss ofperipheral appendages or organs may notnecessarily affect the ultimate functionof circulation, loss of adjacent estuarinehabitats may not depreciate this transportrole of channels ; however, the carryingcapacity and production of the overallsystem (i.e., it's quality) will undoubtedlydecline. On the other hand, significantinhibition of channel habitats' capacitiesto function, 1 i ke arteriosclerosis,will ultimately result in deteriorationof the whole estuary as a healthy, productiveecosystem. It is difficult to understand,then, why channels have typicallybeen some of the most highly impactedhabitats but typically the most ignoredestua~i,ne envi rons when management goalsand priorities are set. Presumably, thedynamics of continuous riverine and marineinfusion of high quality water andorganisms are assumed to naturally mediatethe insults occurring within the estuaryitself or those interjected into the systemfrom upriver or from the ocean. But,as a result, several estuaries in thePacific Northwest have become burdenedwith supposedly innocuous modificationsto the point of disfunction.Of a1 1 estuarine habitats, channelshave undoubtedly been diminished quanti tativelythe least. Bortleson et al. (1980)have illustrated some of the dramaticlosses of subaeri a1 wet1 and habitat (100%in Puyallup River, 99.2% in Duwamish Kiver,and 96.4% in Samish River estuaries)but indicated no losses in channel habi-tat. Thomas' (1982) exhaustive analysisof habitat changes in the Columbia Riverestuary2since 1868 provided an estimate of10.4 km of deep water (>6 m below MLLW)habitat lost since that time. Over theentire estuary, this is a change of only7.3%, as compared to losses as high as76.8% for other habitats (e., tidalswamps). This relatively minor loss ofhabitat applies, however, only to mai nstemand subsidiary channels. Losses of blindor tidal channel habitat are much more extensivebut unfortunately unestimated.Thyas (1982) estimated a 43.2% loss (28.3km ) of tidal marshes in the Columbia River*estuary and Levy (1980a) a 39% (0.23km ) loss of estuarine marshes in theFraser River estuary, but it is impossibleto estimate what portion of these lossesinvolved channel habitats.Qua1 i tati ve changes in estuarinechannels, however, have been rampantsince "civilized" man arrived in the region.Some of these are the, result ofaccretion and erosion unrelated to man'sinfluence, but are symptomatic of thenatural "aging" processes in the evolutionof an estuary. In the more than 100years since the Columbia River estuary wasfirst mapped in entirety, this relativelyundeveloped estuary has undergone somedramatic changes in channel configuration(Fig. 10.1). Certainly changes over thelast forty years can be attributed partially to anthropogenetic a1 terations suchas dredging and dredge spoil disposalwithin the estuary and hydroelectric powerdam construction (and resulting river di s-charge a1 teration) outside the estuary.But it must be remembered that these processesare characteristic of the normalphysical dynamics of an estuary and, althoughthey can be modified by man's

Fig. 10.1. Configuration of channel habitats (>6 m below MLLW) in the Columbia Riverestuary in 1868-1875 (A) and recent time (6); maps modified from Columbia River EstuaryStudy Taskforce (unpubl .) maps prepared for Thomas (1982).118

structures and other manipulations areseldom el iminated. For example, duringthe last 100 years the volume of the MerseyRiver, England, estuary has declinedabou8 10% despite dredging of over 500 x106m of material (Price and Kendrick1963).Physiochemi ca1 attributes such assalinity and their influence upon theestuary's communities have also been alteredover time as a result of the effectof bathemetry upon estuarine mixing andsalinity intrusion. Thomas (1982) theorizedthat more extreme flow fluctuations,extensive shoaling, and a measurablydifferent geomorphology of the entranceto the Columbia River estuary formerlyproduced more temporal ly and spati a1 lyextreme salinity regimes than now exist.The result was probably an essentiallyfreshwater system at all stages of tideduring large spring freshets and increasedsalinity intrusion during periods of lowdischarge; this may have been substantiatedby the reports of significantly brackishwater near Gray's Point in 1805(Thwaites 1959) ; see Fig. 10.1.Qualitative change in estuarine channelmorphology has also changed the demographyof man's exploitation of estuarinefish fauna. This is best illustrated bythe changes in commercial salmon fishingstrategies in the Columbia and FraserRivers estuaries, wherein dredged navi -gation channels can now be fished muchmore effectively by certain net (driftgi 1 lnet, purse seine) fisheries.So man's influence is superimposedupon a natural ly evolving, dynamicsystem. The difference is in theshort-term, intense perturbations mancontinues to impose upon estuaries.10.1 SOURCES AND MECHANISMS OF IMPACTA suite of impacts result from man'sdevelopment of estuaries and their contributingwatersheds. Among the majorperturbations occurring within the channelwhich can produce deleterious impacts tothe estuarine ecosystem are:1) Dredgi ng and dredge-spoi 1 disposal ;2) Filling and other so-called landreclamation;3) Jetty, training wall, and otherconstruction;4) Urban and industrial effluentdischarge;5) Log dumping and storage;6) Commercial or recreational exploitationof fauna and its artificialenhancement; and7) Upstream water diversions and storagereservoi rs.In addition to these, alterations to adjacentestuarine or exogenous riverine orup1 and habitats which indirectly insultestuarine channels i ncl ude:1) Logging;2) Hydroelectric power development;3) Agriculture; and4) Mining.Only the endogenous impacts wi 11 be discussedin this synthesis.Dredging and dredge-spoi 1 disposalhas been probably the most extensive, andoften the most blatant, modification imposedupon channel habitats (Fig. 10.2).Just the magnitude of sediment removal isastoundiny. In the Columbia River estuaryalone, including the mouth and bar, over4.6 x 106m3 of bottom sediment is dredgedannually (based on most recent 5-yeardata, L. Smith, U.S. Army Corps of Engineers,Portland, OR, pers. comm.) or over25% of the estimated annual deposition(Gross 1972). Elsewhere along the coast,1.6 x 106m3 is dredged annually in Oregonestuaries, principally in Coos Bay, theUmpqua River estuary, Yaquina Bay, andSui slaw River e tuary (Smith, pers. comm.) ;about 2.3 x 102m3 is dredged annually inWashinyton State, over half of that inGrays Harbor (Simenstad et a1 . 1982b) ; and0.4 x 106m3 is dredged annually along thenorthern coast of California, almost entirelyin Humboldt Bay (B. Dixon, U.S.Army Corps Enyineers, San Francisco, CA,pers. comm. ).Genera1 1 iterature on envi ronmentaleffects of dredging is extensive (see

Tiq. 10.7. Late It3iiO'

dation of the biological community, althouyhthey are usually manifested overlonger time periods and are Inore effectiveupon communi ty structure due to speciesspecificinteractions. These effects include:1) sublethal decline in waterqual ity (e. g., dissolved oxyyen, turbidity,nutrients, heavy metals, pesticides)or sediment qual i ty (e.y., particle sizedistribution, % volatile solids, depthdistribution and magnitude of redox potential,heavy metals) ; and 2) modificationof current patterns and sal i ni ty intrusionas a result of changes in estuarinebathymet ry.Evaluation of behavioral responsesof aquatic organisms to dredging and theimp1 ications to their ultimate survivalhas seldom been attempted, however. Evenin the absence of any sublethal effectsto dredge-suspended sediment (i.e., Kehoe1982), organi scns such as juvenile Pacificsalmon, which depend upon channel habi -tats as migration corridors, may activelyavoid certain turbidity levels (Bissonand Bilby 1982) to the detriment of theirability to feed effectively or to avoidpredators.Fi 11 ing and diking have obvious directeffects by removal of blind (tidal)channels which characterize tidal marshand swamp habitats. This has been apervasive modification of many PacificNorthwest estuaries (Fig. 10.3) and, giventhe apparent dependence upon these shallowchannel systems by certain juvenilesalmonids (see Sect ion 6.2; Levy et dl.1979; Anderson et al. 1981; Levy andNorthcote 1981; Congleton et al. 1982;Levy and Northcote 1982; Levy et al.1982), the removal of such optimal habitatsmay be a major contributor to thedecline of many native salmon runsthroughout the region.In addition to the direct el iminationof channel habitat, the constructionof structures such as dikes, jetties, andtraining walls in or adjacent to channelsoften impose far-reachiny effects uponestuarine ci rculation. Current velocitiesand salinity intrusion are commonlyaltered as a result of flow constrictionOr inhibition, resulting in direct modificationof the behavior of organi s~ns andcommunities lirni ted to specific currentvelocity and sa l inity regisles or i ndi rectimpact by loss of food resources or refugia.Levinys and Chang (1977) comparedCurrent velocities in a "back channel"(Wi 1 liamson slough; 60 cat S~C-I),withininfluence of a winy darn (Steveston Is1 and;75 cm sec-I), in mid-channel (LadnerReach; YO cm sec-I), and adjacent to atraining wall (Woodward; 104 cm sec-1) inthe Fraser River estuary dnd found significantdifferences due to the influence ofthe training wall althouyh not of the wingdam. Interpretation of Brett's (1970) andBrett and Glass' (1973) response surfacesfor critical swimming speed of juveni lesockeye salmon would suggest that feedingactivities under temperatures expectedduring estuarine outmi gration i nvol ve sustainedswimming speeds of under threelengths sec-1. Extrapolating their relationshipsto the expected lengths of otheroutrni yratiny salmon species, it wouldappear that normal feeding behavior wouldbe disrupted at water velocities yreaterthan 40 cm sec-1. Levinys and Chang(1977) also suggested that important preyof juvenile salmon. such as the qamrnaridconfervi cof us, wouldremaininq on the bottomor attach& to algae at cirrent velocitiesgredtzr than 10 crn sec-1; Levings(1973) found that much higher, sustainedvelocities (a250 cm sec-I) woul d actual lyflush A. conferivicolus out of the innersquamiTh River estuary. This il lustrateswhat may be an element of the functionalrelationships between water velocities,prey avai 1 abi 1 i ty , and foraging behaviorof juvenile salmon. The fact that juvenile salmon do, indeed, feed predorninantlyin subsidiary and blind channels wherethe highest standing Stock of benthic,epibenthic, and drift prey are found, i l-lustrates the potential deleterious ef feetof increasing channel water velocities inthese habitats.~odi fication of current velocitiesalong the bottom and the resulting restructuringof bottom sediments can alsolead to shifts in trophic associations ofbenthic infauna. Mildish (1977) and

Fig. 10.3. Exampleofwheredikingand filling have removed (blindor tidal) channelhabitat in Fraser River estuary; (A) illustrates diking of subsidiary (entering fromlower right) channel and blind channels in saltmarsh, and (8) shows historical channelpatterns still evident in existing fields (photos courtesy of David Levy, WestwaterResearch Centre, Universi ty of British Columbia, ~anada) .

Wildish and Kristiqanson (1979) hypothesizedthat the magnitude of turbulent liasstransfer fro111 the water co1u:nn to thesediment surface determines the proportionof filter feeders to deposit feeders.They suggest that, at least under food1 imi ted situations, deposit feeders predominatein low current speeds and filterfeeders are benefited by moderate to hiyhcurrents and bottom roughness. Such inducedchanges in water velocities andsalinity intrusion probably also affectthe rate and distribution of detritusaccumulation or processing. The end resultof this perturbation would bedisplaced, if not reduced, sources offood for detritivorous organisms in thechannel habitat.Estuarine channels have traditional -ly been looked upon as opportune receptaclesfor urban and industrial wastes dueto their usually close proximity to effluentsources and rapid mixing potential.A1 though there is some consequenti a1urban and rural drainage into subsidiaryand blind channels, most of the massivewaste discharges occur in mainstem channels.But even these dynamic habitatshave a threshold to the amount of wasteswhich can be accommodated without changesto biological structure. Two categoriesof comnon wastes--organic and toxicant--ref1 ect the mechani sms of impact uponchannel habitats and associated biota.Organic pol lution is manifested primarilythrough increased chemical or biologi c.31oxygen demand within the water columnand, with settlement of organic particles,on and within bottom sediments.Since dissolved oxygen is a criticalrequisite for estuarine oryanisms' (excludingsome mi crofl ora) rnetabol i sm (seeVernberg and Vernberg 1972 for review),even minor short-term depressions cana1 ter animal behavior and major, 1 ong-termdeclines can result in major communityshifts toward a reduced number of moretolerant species. At sufficient concentrations,toxicants such as petroleumhydrocarbons, heavy metal s, radioactiveisotopes, pesticides, acids, and otherchemicals have the potential to directlyki 11 aquatic organisms (i e., acutelytoxic); but more often than not they arepresent in chronic sub1 ethal concentrationswhich still influence the distributionand abundance of organisms throughdegradation of longevity , reproduction,growth, metabol ism, and behavior.Further, more detai led examinationsof pollutant effects upon aquatic organismsand communities can be found inreviews such as Bryan (1971) and Warren(1971). Felice (1959) also described aclassic case of the influence of domesticand industrial wastes upon the benthiccommunity of San Francisco Bay, an estuarywith many para1 lel features to PacificNorthwest estuaries. Anderson et a1 .Is(1981) examination of the envi ronmentaleffects of harbor construction at Steveston,Hritish Columbia, also indicates thesynergistic influences of normal envi ronmentalperturbation, organic pollution,and dredging and jetty construction onendemic channel communities.Log transportation ("booming"), dumping,and storage has been a traditionaluse of estuaries in this region. Forexample, logs from all along the BritishColumbia coast are transported to theFraser River estuary, where almost 5 km2of estuarine habitat, most of its shallowreaches of mainstem channels, are developedas "booming grounds" to hold a sixweeksupply of logs for the local saw andpul mills (Levy et al. 1982). Approximately1.2 km2 of the Columbia Riverestuary is presently utilized for logstorage (Pac. NW Riv. Basins. Comm.1980).Many studies of the envi ronmentaleffects of log handling and storaye inestuaries have been conducted within theregion (Schaumberg 1973; Schuytema andShankland 1976; Smith 1977; Conlan andEllis 1979; Sibert and Harpham 1979;Zegers 1979; Levy et al. 1982) and inAlaskan estuaries (Ellis 1970; Pease1974; Buchanan et al. 1976; Schultz andBerg 1976), while many of the negativeimpacts documented were particularlyassociated with 1 i ttoral habitats, wheredirect benthic disturbance was caused bygrounding logs, log dumping, rafting, andstorage in subsidiary and shallow regions

of mainstem channels can also produce significaritirnpacts if water exchange fromtainly played a role in most cases. Giventhe important role which these consumerriver and tidal currents was low. These organisms (typically upper trophic levelwere primarily due to the accumulation of carnivores) have upon the structure ofbark and log debris on the bottom, caus- channel communities, it may be valid toing smothering of benthic organisms and assume that ecol ogical accommodation hasmeasurable increases in biochemical oxy- resulted in somewhat di fferent producergen demand in the water overlying the and primary consumer assemblages thandebris. Leachates from stored logs and occurred historically. Pacific salmon,bark deposits may also locally degrade northern anchovy, Pacific herring, andwater qual i ty through either direct Dungeness crab are examples of exploitedtoxicity or via biological and chemical species which are suspected to structureoxygen demand (Pease 1974; Buchanan et their prey assemblages (see Secfion 9.2);al. 1976; Peters et al. 1976), factors and it must also be concluded that assowhichmay be intensified by intermediate ciated pelagic, epibenthic, and benthicsalinities (Pease 1974).assembl ayes have a1 so responded indirect-1y to man's exploitation of these preda-Prolonged impacts upon benthic com- tors. The consequence of the recent enmunitiesresulting from loy rafting is hancement efforts upon some of these speoftenmanifested in reduced standing crop cies, i.e., Pacific salmon, or the protecanddiversity and tends to be restricted tion of other, previously-harvested predatobenthic infauna rather than epibenthic tors, i.e., seals and sea 1 ions can alsoorganisms except under extreme situations. be predicted to induce measurable changesFor example, Smith (1977) illustrated in the community because of increased prethatthe abundances of three polychaete dation upon their preferred food organannelidspecies (Mana unkia aestuarina, isms. This has been suggested for hatch-Pseudoam hicteis Ca itella ery releases of juvenile salmon in Hood&ubiferous a m p h i p o h Canal (Sinenstad et al. 1980) and night7ie- p ium salmonis), and oligochaetes were also be applied to increased seal and seareducedinraft areas of the Snohomish lion predation upon crabs and fishes inRiver estuary, but the epibenthic amphi- the Columbia River estuary (Beach et al.pod Eoyammarus confervicolus was unaffect- 1981). Such holistic food web interaced.Levy et al. (1982) indicated that tions must be equally considered synerepibenthicqysids (Neom sis mercedis) and gistic with man's other impacts in estuaramphipods(E. confervlco -5- us and Corophium ine channels and, ultimately, within hissp. ) were erther more or equal ly abundant management strategies for the maintenanceand isopods (Gnorimosphaeroma ore onensi s) or restorat ion of a speci f i c estuarineless abundant in the Point G r e h -age area as compared to the Musqueam Marsachannel community.control area; environmental conditions, 10.2 UTILIZATION OF AND DEPENDENCE ONt~owever, were responsible for some of CHANNELS BY ECONOMICALLY - AND ECOthesedifferences, and no si gni f i cant con-LOGICALLY-IMPORTANT SPECIEStrasts in growth of chinook salmon frywere evident between the two study areas As illustrated throughout this syndespitequal i tati ve differences in the thesis, many organisms of economic importfishes'diets.ance to man or of ecological importanceto the estuarine ecosystem can be foundA final, seldom-considered and even1 ess-evaluated impact upon channel communutilizingchannel habitats. But in thecontext of estuarine management, the cri t-ities is that of extensive exploitation ical question is dependence upon channelsof economical iy-important species. Whi le to sustain popul ati ons of these organismshabitat reduction or alteration has cer- by providing ample food resources, optitainlycontributed to the decline of many mum conditions for growth and/or reproducofour cornnmercial or sport fish and in- tion, and refugia from predation. Such avertebrate stocks, overharvesting has cer- definition of uti 1 ization in terms of124

estuarine channels as "critical " habitatsrequires more knowledge of the functionalrelationships regulating populations thanis usually available.Util ization of estuarine channel s isobvious for many econmical ly- and ecol ogi -cal ly-important species of fishes. But,among these, only a few can be illustratedto be potentially limited by the availabilityor quality of estuarine channelhabitat. Juvenile salmon such as chinookand chum may provide the best example ofsuch a positive functional relationshipbetween estuarine residence and popul a-tion production (see Section 6.2.2). Thismay also be the case for Pacific herring(Pearcy and Myers 1974), American shad,and striped bass. 8ut there is some evidencethat many species "utilize" offshoreenvirons to a yreater extent thanestuaries and, as such, occurrence inestuarine channel s is merely a product ofcurrent transport of planktonic larvaefrom a large offshore population into theestuary; this may be true of northernanchovy, surf perch, Pacific sand lance,lingcod, English sole, butter sole, andsand sole (Pearcy and Myers 1974). And,while the ecological ly-important Crangonspp. shrimps may be highly dependent uponestuarine channel habitats, there is noevidence i 1 lustrating that channels providecritical habitats for economical lyimportantDungeness crab as juveni 1 es,which may be equally or more abundantoffshore.A number of ecological ly-importanttop carnivores such as seals, sea lions,and many of the surface and diving waterbirdsare seasonal migrants which behavioral1y immigrate to estuarine channel sfor specific periods of the year. Sincethere is good evidence that this is associatedwith optimum foraging and/or reproductionconditions, their population levelsmay also depend upon this utilizationpattern.10.3 RATES AND PATHWAYS OF RECOVERY FROMSHORT-TERM IMPACTSA1 though some manipulations of channelssuch as extensive dredging can bedramatic in their initial impact, if sustainedfor only a short interval, biologicalrecovery may also involve only a relativelyshort time period. Although unverified,it may be assumed that, due torapid mixing and immigration of pelagicorganisms, impact to water column assemblageswill be relatively short-1 ived.Benthic and epibenthic assemblages, onthe other hand, wi 11 require longer recoverytimes and may pass throuyh a numberof successional stages before attaininypre-impact status. McCauley et al.(1977) documented a readjustment in benthicinfauna within a dredged area ofCoos Bay, Oregon, after 28 days and withinimpacted, adjacent areas after 14days; similarly, infauna at the site ofdredye spoi 1 disposal had a1 so recoveredfrom depletion within 14 days. Andersonet al. (1981) described recovery of thebenthic community in Steveston Harbor inthe Fraser River estuary within one monthafter dredging. McCauley et al. (1976)also followed the recolonization patternsof four species of polychaete annelids inCoos Bay, Oregon, for eight weeks aftermaintenance dredyi ng. They found thatCapi tell a capi tata -domi nate-d the assemblaqein recently de~osi ted sediments butnot- under si tuition; of rapid sedimentturnover; Polydora liyni, on the otherhand, pervaded where sediments were overturnedfrequently and where sawdust andwood debris occirred. Steblospio benedicti and Pseudoool . " vdora kemoi are commonunder either recent sedimeaon or sedimentoverturning, perhaps because bothcan readily vacate their tubes to rebuildnew ones quickly. Thus, the rate and patternof recolonization will proceed as afunction of the rate of sediment resuspensionor sedimentation as well as the organiccontent (Be1 la and W i 11 iamson 1979-1980; see also Section 2.5.2). Pequegnat(1975) suggested that mei ofaunal consti tuentsof the benthos may be even more sensitiveto sediment disruption, as evidencedby changes in generation time,standing stock, and diversity. A1 though

they may be the first colonizers, theiri ntirnate re1 atiotiships with sediment propertiesand intrinsic short populationcycles would dictate that succession ofmeiofauna assemblages would be prolongedas long as abnormal sedimentation (orremoval ) persisted.Unfortunately, such successionalpatterns have not been well documented indredgi ng-impact studies in this region.Oliver et al. (1977), however, providedan excellent illustration of benthicsuccession in a soft-bottom assemblage ofsmall crustaceans and polychaete annelidsin Monterey Bay, California. Two phaseswere evidenced after dredging ceased.The first involved immediate immigrationof peracarid crustaceans and settlementof larvae of opportunistic polychaetespecies, i.e., relatively small-sizedtaxa with short generation times, lowfecundity, and high larval avai labi lity.The later phase included gradual reestab-1 ishment by less motile crustacenas andless opportunistic polychaete species.One important thing to remember inconsiderf ng succession rates and patternsin the temperature waters of the PacificNorthwest is the highly seasonal reproductiveschedules of most fauna. As a result,succession is going to be highlymediated by the seasonal availability ofpropagules of these opportunistic and latersuccessional stage taxa. In addition,benthic asse~nblages in central regions oflarge estuaries like the Columbia and FraserRivers may never naturally progressbeyond the opportunistic species successionalstage. Due to the frequent .andoften extreme fluctuations in salinityregimes, these benthic assemblages aretypically limited to species which areto1 erant of such random environmentalperturbations and persist by being small,capable of wide dispersal and rapidreproduction, and extremely euryhal ine.10.4 METHODS OF CHANNEL RESTORATION ANDREHABILITATIONUnlike the recent support for estuarinemarsh restoration (Josselyn 1982; butsee Race and Christie 1982 for caveats),restoration and rehabi l i tation of channelsis seldom considered among available optionsin estuarine habitat management.Dorcey et al. 's (in press) analysis ofthe history, status, and managementoptions of estuarine sloughs, specificallyTilbury Slough in the Fraser Riverestuary, presents one of the few discussionsof restoration and enhancementstrategies applicable to such estuarinechannel and associated habitats (e.g.,marshes). Among the rehabi 1 i tationoptions specific to the area's channelswere: 1) breaching of remnant dykes toincrease flushing and passage of juvenilesalmon; 2) dredging of the mouth and channelto arrest infilling and maintain circulation;3) dredging of side (blind)channels to increase juvenile salmon utilization;and, 4) stabilization of waterlevels through flow control structuresand selected channel creation.In addition to these means of restoringthe habitat to a viable, productiveenvi ronment , management must i nvol ve removalor mediation of the sources of degradationand protection of the selfcleansingmechanisms. In the case ofTilbury Slough, as in many similarlydevelopedestuarine channels in thePacific Northwest, exogenous influencessuch as pollutant sources eliminate someof the more viable options (i.e.,openingup flow from the former, upriver end ofthe channel), In all cases, however, restoration- must be accompanied by changesin those uses which led or contributed tothe channel's deterioration. Pollutantsources must be eliminated or diverted.Structures (i.e., docks, training walls,wharves) and practices (i.e. , log dumpingand storage) which promote abnormal sedi -mentation and scouring must bediscouraged.There are presently active managementpolicies promoting or practicingmitigation as a means of compatibly incorporatingnecessary estuarine developmentinto the natural environment withoutprecluding such activity (Ashe 1982). Assuch, mitigation can take on two goals:1) the creation, restoration, or enhancementof an estuarine area to maintain the

functional characteristics and processesof the estuary; and, 2) the creation orrestoration of another area of similarbiological potential to ensure that theintegrity of the estuarine ecosystem ismaintained. While the first goal iscompatible with maintenance of a viablyfunctioningestuarine channel community ,the second yoal should be approachedjudiciously. Destruction or debi 1 itativemodification of any natural habitat,particularly channels so integral to anestuary's circulation, by creation of asupposedly equivalent habitat cannot bejustified with the existing technology.This approach to mi tigation originatedfrom relatively successful salt marshrestoration projects in east coast estuaries,but man-made marshes in west coastestuaries have yet to be proven comparablereplacements for natural marshes (Raceand Christie 1982). A1 though restorationof diked, filled, or modified channels isa worthwhile objective of contemporaryestuarine manayement, devaluing existingchannels in exchange for the unpredictableresults of these projects is still adubious strategy.10.5 RESEARCH GAPS AND PRIORITIESDespite the profusion of knowledgeof estuarine channels in the PacificNorthwest, i 1 lustrated by the bulk of theLiterature Cited section, we find our understandingof the role of these habitatsin the estuarine ecosystem to be limited.In most cases this is because this vastaccumulation of data is predominantly descriptiveand qua1 itative. That which isquantitative is typical 1 y oriented towarda particular taxa and seldom of a scopeencompassing other organisms of the community,environmental conditions, or functionalre1 ationshi ps among them. Futureresearch must address this lack of holisticapproaches, particul arly when evaluatingthe dependence of important biotaupon key functional processes. Despitethe intent of this synthesis to identifythe role of estuarine ci rcul ation, sal initygradients, nutrient and material fluxes,and sediment structure in determi ni ngthe composition, distribution, and standingstock of estuarine biota (Section1.1), few such functional relationshipshave been verified though many have beenhypothesized. The fol 1 owing research proposalsare designed to elucidate, test,and quantify these "conceptual hypothesismodels" in terms of the functioning ofestuarine channel systems, their relationshipto overall estuarine processes, andthe imp1 i cations of estuari ne manayementoptions.1. Prepare comprehensive analysis ofhi storical trends in channel habitatdemography (extent and morphology)for all major Pacific Northwest estuarieswhere data exists; i nterpretdocumented changes re1 ati ve tonatural and anthropogeni c processes.Vertical 1~-strati fied, three-dimensionalmathematical modeling of ci r-cul ation in a prominent, representativePacific Northwest estuary shouldbe conducted with considerable fieldcalibration in order to better understandthe effect of river dischargeand estuary bathymetry upon salinityintrusion and sedimentation. Variousdevelopment scenarios affecting parameterssuch as riverine discharge(i.e., dams), bathemetry (i.e. ,dredging), or geomorphology (i .e. ,jetty construction) could be simul atedfor optimum assessment of effectsupon circulation.3. Conduct intensive, vertical ly-strati -fied sampling of pelagic and epibenthiczooplankton over diel periodsat representative channel 1 ocationsthrough the estuarine gradient. Ifperformed concurrently with fieldcalibration of the three-dimensionalcirculation model (#2 above), the re-sul ting documentation of diel patternsin zooplankton distribution andstanding stock could be correlatedwith cycles in tidal and current velocity,salinity distributions, andmi xi ng processes.4. As in Healey's (1982) estimation ofthe ultimate (i.e.,to adult return)survivorship of chum salmon uti 1 izingthe Nanaimo River estuary, the

e1 ati ve importance of estuarinechannel attributes must be evaluatedin terms of the total cost to thesalmon population. Similarly, differentpatterns of channel uti 1 izationby juvenile salmon (e,g., extendedresidence, inshore/offshoremovements) must be examined relativeto these attributes. A1 though thereis often opportunity for "natural 'Iexperiments, the lack of control overdependent variables often inhibitsinterpretation. For this reason,manipulation experiments should beundertaken to isolate independentvariables affecting patterns of channelutilization. Examples includeequal releases of marked groups offish at different points along theestuarine gradient or differentdensity or fish-size releases justupstream of the estuary and recaptureof the marked Fish at the mouthor just outside the estuary.Uespi ti? strony evidence that foodwebs of estuarine channel comtnunitiesare based yredomi nantly upon detritus,there is 1 i ttle data substantiatinythis hypothesis (see Section9.1). Techniques such as stable carbonisotope analysis should be appliedto primary producers, inputsof dissolved and particulate organicand dl ssol ved inorganic carbon fromexogenous sources, detritus accumulations, and dominant consumer organismsin estuarine channels in orderto evaluate the sources and pathwaysof organic carbon leading to theendemic food web.Siini l ar to determining causal mechanis111~of utilization of estuarinechannels by juvenile salmon (#4above), the factors influencingstructure, distribution, and standingstock of benthic and epibenthicassernbl ages cannot be easily eluci -dated from highly variable fieldmeasurements ; separation of confoundingeffects of natural physical andcnerni cal influences from those ofpol lution are also usually intractable.Functional relationships be-tween physiocherni cal variables andlarval settlement, feeding and othercritical behavior, reproduction, andsurvival can be resolved only throughexperimental means. Organisms suchas polychaete annelids, harpacticoidcopepods, gammarid amphi pods, mysids,and crangonid shrimps should be testedunder control led rep1 icatable conditions indicative of estuarine channelbenthic environs, both as individualspecies and 1 ife historystages as well as characteristicmixed-taxa assemblages. This approachachieves i ts ul timate appl i-cabil ity in the form of ecosystem~~iicrocosms which, dl though subject toa nunber of shortcwings (Harte etal. 1980; Silierlstad et al. 1982) canbe a very effective method of environmentdlilnpdct assessnent and ecologicalelucidation (T.P. Smith1980).7. The importance of the null zone inthe concentration of detritus hasbeen suggested by studies of watercolumn primary production and bothpelagic and epi benthic zoopl ankton(see Chap. 5). But the processesaccounting for detritus entrainmentand processing in the nu1 1 zone ofthe region's estuaries are littleunderstood. Both vertical and hori -zontal distributions of detritus particlesand associated water chemistrycharacteristics (i.e., DOC, DON, ATP)should be sampled seasonally in relationto circulation parameters in anestuary with a we1 1 -defined nu1 1zone. As in documenting zooplanktondistribution processes (#3 above),coup1 ing with the three-dimensionalci rcul at ion model (#2 above) wouldalso expand the potential of similarlyexplaining detritus cyclingand utilization by physical ci rculationprocesses.Appendix D provides a list of researchgroups/organi zati ons currentlyconducting research in estuarine channelhabitats in the Pacific Northwest.

10.6 SUMMARYAlthough they are classical ly avoidedin most research, due to the complexityand dynamic nature of the physiochemi calenvironment, channel habitats in PacificNorthwest estuaries obviously supportunique populations of economical ly- andecological ly-important biota. This bondingtakes form as routes for organismmovement and migration, conduits ofmaterial transport, and sources ofrep1 eni shment for sediments, nutrients,food particles, and organism recruits.A1 1 estuarine habitats are integratedthrough the estuary's articulated systemof mainstem, subsidiary, and blind channels,and the principal linkages withterrestrial and marine ecosystems occurthrough the mainstem channels. Inaddition to this critical role as theestuary 's ci rculatory system, channelsact as critical nursery habitats fororganisms such as juvenile Pacific salmonand Pacific herring; as opportune f6ragingand resting habitats for migrantbirds and marine mammals; and as thefocal point of detritus entrai nment,accumulation, and processing in theestuary.Management of any estuarine resourceor exogenous resources which derivebenefit from a we1 1-functioning estuarycannot occur without consideration andmanagement of estuarine channels. Butthe state of our knowledge of estuarinechannel communities and processes and oftheir management is lagging far behindthat of the other major estuarine habitats.This document describes whatDorcey ahd Hall (1981) would define asthe "descriptive knowl edge" necessary forinput into management decisions. Unfortunately,there is also a second categoryof requisite information, that of the"functional knowledge" of how the channel'sbiotic and abiotic processes operateand interact, which we have barelybegun to develop. Essentially all thestudies described herein have beenderived from inventorying or monitoringtypes of investigative activities. Anyinterpretation of system processes hasmerely been the result of deductive analyses.Genuine functional knowl edye requiresa different approach, that of generating testable hypotheses and experi -rnents. Such experimental research offersour only view of causal mechanisms, andthe process of sequential ly testing a1 ternativehypotheses is our only means of'exploring the complex interrelationshipsaffecting channel communities. Effectivemanagement decisions require this functionalknowledge and, as advocated byDorcey and Hal 1 , experimental managementand research are the only source of functionalknowledge. It is hoped. that, inaddition to synthesizing our descriptiveknowl edge of estuarine channel communitiesin the Pacific Northwest, this' communityprofile might provide the impetus forthe necessary steps to the experilnentswhich are ultimately necessary for effectivemanagement of our region's estuaries.

LITERATURE CITEDAges, A. 1979. The sal ini ty intrusion inthe Fraser River: sal in1 ty, ter~peratureand current observations, 1966, 1977.Pac, Ilar. Sci. Rep. 79-14, Inst. OceanSci., Patricia Bay, Sfdncy, B.C.,Canada, 193 pp.Ayes, A,, and A. Woollard. 1976, Thetides in the Fraser estuary. Pac. tlar.Sci. Rep. 76-5, Inst. kean Sci,, PatriciaBay, Vfctoria, B.C., Canada.108 pp*A1 banese, J.R, 1979. A sl~nulation siodelfor coas tit1 zoobenthic ecosystems.Ccnt. Ecal . tbdel, Rep, 6. RensselserPolytechnic Inst., Troy, N.Y. 46 pp.Prnerlcdi~ Eeol og ical fnstl tute. 1976.l~lctlonary of geoloq4cal terns, Rev.od, Anchor Press, Garden City, N.Y.472 pp.Mi Test, Enc. 1981. Chantcal testing ofsedttaents .in Grctys Harbor, Mashing tan,Rep, to Seattle District, tJ,S. ArmyCorps of Eny),, Environ. Res., Seattle,Wash, 112 pp.I. U, B J rtwel 1 , S. C, flyers,A,V, ilincks, and G.W. O'Connell. 19C1.Envl rormentdl effects of harbor constructionacrfvf ties at Steveston, BritistiColumb9d. Parts 1 to 3. Can. Tech.Rep. Fish. Aquat. Sci. 1072, Dep. Fish,kesns, West Vancouver, B.C., Canada.41 PP.AnQe eon, E.P.,Anderson, G.C. 1972, Aspects of marinephytoplankton studies near the Go-1 ruabiaRiver, wltk specidl reference to a subsurfacechl orophyl 1 maximum. Pages219-240 A.T, Pruter and D.L. Alverson,eds, The Colmbfa River estuaryand adjacent ocean waters : hioenvironnentalstudies. Univ. Wash. Press,Seattle.Anlta, N.J., C.D. tfcAllister, T.R.Parsons, K. Stephens, and J.D.H. Strickland.1963. Further measurements onprfnary production using a large-vof uneplastic sphere. Limnol. Xeanogr. 8:166-183.finraku, N., and ?4, hori. 1963. Prcl ininarysurvey of the re1 at ionship betweenthe feeding habit and the structure ofthe mouth-parts of marine copepods.Lfmnol. Oceanogr. 8:116-126.Antonel i s, G.4., and C.H. Fiscus. 1980.The pinnfpeds of the Cal ifornia Current.Cal if. Coop, Oceanic Fish. Invest.,CALCQFI Rep. 21: 68- 78,Anstrong, D., 0. Stevens, an4 J. Hoeman.1982. Dlstribut ion and abundance ofhngeness crab and Crangon shrimp, anddredging-re1 ated mortal i ty of invertebratesand fish In Grays Harbor, Washington.Final Rep. Seattle Dist., U.S.Amy Corps of Eng. and Wash. Oep. Fish.349 pp.Arthur, J.F., and M.Q. Rat 1. 1979. Factorsinfluencing the entrapment of suspendedmaterial in the San FranciscoBay-Del ta estuary. Pages 143- 174 .in-T.J. Conmos, ed, San Francisco Ray:the urbanized estuary. Cal if. Acad,Sci., San Francisco.Ashe, D.M. 1982. Fish and wild1 ife mi tigation:description and analysis ofestuarine appl ications. Y.S. Thesis.Inst. %re Stud., Univ. Wash., Seattle.123 pp.

Avnimelech, Y., 8.W. Troeger, and L.W.Reed. 1982. tklutual flocculation of algaeand clay: evidence and impl ications.Science 216:63-65.Barber, R.T. 1966. Interaction of bubblesand bacteria in the formation oforganic aggregates in sea ~tater. Nature211:257-258.Bax, N.J. 1982. Seasonal and annual variationsin the lnovement of juvenile chumsalmon through Hood Canal, Washington.Pages 208-218 in E.L. Brannon and E.O.Salo, eds. proceedings salmon and trout!ni gratory behavior symposium, June 3-5,1981. School Fish., Univ. Wash.,Seattle.Bayer, R.D. 1978. Aspects of ah estuarinegreat blue heron population. Pages213-217 A. Sprunt, IV, et al., ods.Wading birds. Res. Rep. 7, Natl. AudubonSoc.Baylor, E.R., artd W.H. Sutcliffe, Jr.1963. Dissolved organic matter in seawateras a source of particulate food.Limnol . Oceanoy r. 8: 359-381.Beach, R.J., A.C. Geiger, S.J. Jeffries,and S.D. Treacy. 1981. Marine manmalfisheryinteractions on the ColumbiaRiver and adjacent waters, 1981. SecondAnnu. Rep., Nov. 1, 1980-Nov. 1, 1951.Wash. Dep. Game, Wildl. Manaye. Div.,Olympia, Wash. 186 pp.Beardsley, A.J. 1969. Movement and angleruse of four foodfishes in YaquinaBay, Oregon. Ph.D. Thesis. Oreg. StateUniv., Corvallis. 185 pp.Beccasio, A.D., J.S. Isakson, A.E.Redfield, N.M. B1 aylock, f-1.C. Finney,R.L. Frew, D.C. Lees, D. Petrula, andR.E. rfidwin. 1981. Pacific coast ecologicalinventory --useris guide andinformation base. U.S. Fish Wildl.Serv. Biol . Serv. Program FWS/OBS-81/30,Washington, D.C. 159 pp. + maps.Bella, D.A., and K.J. Williamson.1979-1980. Diagnosis of chronic impactsof estuarine dredging. ,I. Envi ron.Syst. 9(4):289-311.Ceyer, F. 1958. A new, hottorn-livinqtrachyrnedusa from the Oslo fjord. NyttMag. Zoo7 . 6: 121-143.Bigg, M.A. 1969. The harbor seal inBritish Columbia. Fish. Ses. Board Can.Bull. 172.Bisson, P.A., and R.E. R i l by. 1982.Avoidance of suspended sediment Sy juvenilecoho salmon. N. Am. J. Fish.Manage. 4: 371-374.Blackburn, J.E. 1973. A survey of theabundance, distribution and factors affectingdi'stribution of ichthyo~lanktonin Skagit Bay. M.S. Thesis. Univ,Wash., Seattle. 136 pp.Blahm, T.Y. 1979. Effect of agitationdredging on benthic communities, waterquality, and turbidity at Chinook Channel.In Propeller wash agitation dredqing,(5Tiinook Channel, Washington. Nav.Div. Res. Eva1 . Rep. 2-79. U.S. ArmyCorps Eng., Portland, Oreg. 19 pp.Blaylock, W.M., and 3.P. Houghton. 1981.Commencement Bay studies, technical report.Vol. 4: Invertebrates. Rep. toU.S. Army Corps Eng., Seattle, Distr.,Dames and Moore, Seattle, Wash. 58 pp.l3l azevich, J.V., A.R. Gahler, G.J. Vasconcelos,R.H. Bieck, and S.V.W. Pope.1977. Monitoring of trace constituentsduring PCB recovery dredging operations:Duwamish waterway. Rep. EPA/910/9-77/039. U.S. EPA, Surveil. Analy. niv.,Seattle, Wash. 156 pp.Boggs, S., and C.A. Jones. 1975.Seasonal reversal of flood-tide dominantsediment transport in a small Oregon estuary.Bull. Geol. Soc. Am.878:419-426.Bell, S.S., and K.H. Sherman. 1980. A Boley, S.L., R.Z. Conrow, R.T. Hudspeth,field investigation of meiofaunal dis- S.P. Klein, H.L. Pittock, L.S. Slotta,persal : tidal resuspension and imp1 ica- and K.J. W i l l iamson. 1975. Phvsicaltions. Mar. Ecol. Prog. Ser. 3:245-249. characteristics of the Youngs Bay estu-131

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APPENIX AGlossary 9f Terms

Advection - Local change in a property ofa system that takes place as a resultof a current, as of air or water;inc 1 udes transport of water vapor,heat, sediment load, salinity(Proctor et al . 1980).Alkal inlty - The capacity of a water massto accept protons, i.e., hydrogenions.Anadror~ious - Mi grating up rivers from thesea to breed in fresh water.GLOSSARY OF TERMSBenthic - Relating to the bottom of thebody of water, i.e. animals, livingwithin or directly upon the substrate.Benthivore - Oryanism which feeds onbenthic flora and fauna.Bight - A bend, curve, or indentation inthe shore of a sea, including thebody of water bounded by such acoastal form.tomoos ng Branching , Boulder - Rock fragment wi di ameaerinterco~;r;runicating, thereby producing larger than 60.4 cm (Cowardin et al.a nctlike or braided appearance. 1979).Anyul ar - A roundness yrade showing verylittle or no evidence of wear, withedges and corners sharp (Am. Geol.Inst. 1976).Autotrophic - Self-nourisning; referringto organisms that are capable of constructingorganic matter with hi yhenergybonds frodl inorganic substancesfor their food supply by photosynthesisor ct~emosynthesi s.Uar - An elongated landform generated bywaves and currents, usual ly runningpara1 1 el to shore, composed predomi -nant ly of unconsol idated sand,grave 1, cobbles, stones and rubbleand with Mdter on two sides.Bed - Bottom of the channel.Cavitation - Corrasive and corrosive effectof collapsing of bubbles producedby a decrease of pressure toincrease of water velocity (Bernouli ieffect) at point where pressure isincreased to decrease of velocity(Am. Geol. Inst. 1976)Channel - An open conduit either naturallyor artificially created whichperiodical ly or continuously containsrnovlng water, or which forms a connectinglink between two bodies ofWater (Langbein and Iseri 1960).Channel Bank - The sloping land borderinga channel, which typically has asteeper slope than either the bottomof the channel or the adjacent land(Cowardin et al. 1979).Bed Load - Sediment particles and other Cobble - Rock fragments with diametersdebris rolled alony the bottom by between 7.6 cm and 25.4 cm (Cowardinrnovlng water. et al. 1979).

Competence - Maximum size of particles of iletritds - Finely divided naterial of orgivenspecific gravity which a water ganic 3r inorganic origin which ismass will move at a given velocity. either suspended in the water coluriln or,in the case of large particles, accurnu-Consumer - Heterotrophlc orqani - sm, chief lv lated on the hotton.animals, which ingest other organismsor particulate organic matter.Diffusion - The spreading out of molecules,atoms, or ions in a waterCoriolis Effect - The effect of themass in directions tending to equalearth'srotation to deflect waterize concentrations in all parts ofmasses to the right in the northernthe system.'phere and to the left in thenorthern hemisphere.Diversity - Term or lneasure used to describe the species-abundance di s-Corrasion - Mechani cal erosion performedtribution of a biotic assemblage orby moving agents, generally by thecommunity; both the number of speciesand tne evenness of their abunirrlpactor grinding action of partidancescontribute to the termcles in water.(Pielou 1977).Corrosion - Chemical erosion which resul tsfrom the reaction of water and rockson the surface of the land.Critical Erosion Velocity - Lowest velocityat which grains of a given size,loose on the bed of a channel, wi 11move.Decomposer - An organism that breaks downdead organic matter into simpler constituents for its nutrition.Uernersal - Nektonic fauna living on orclosely associated with the bottom;typical ly refers to fishes, whereepi benthic refers to invertebratefauna.Dendri tic - A drainage pattern chardcterizedby irregular branching in alldirections with the tributaries joiningthe main channel at all angles(An. Geol . Inst. 1976).Density - Abundance of organisms per unitarea or volume.Deposit Feeder - Organism, typically benthic,which is either somewhat selectiveor almost completely unselectivein feeding; includes organisms whichsweep the surface or use ciliarytracts along extensile tentacles.Elutriate - Tne fluid product of mixingwater, or a water acid solution, withsediment, a1 lowi ng settl iny over avarying amount of time and decantinythe resultiny solution,Epibenthic - Associated primarily withthe surface of the bottom but alsowith the water column directly abovethe bottom.Euhaline - Associated with nrouth Or extremesalinity, i.e., 30-40 ppt,region of estuary (Symp. Class.Brack. Mat. 1959).Facultative (Feeder) - An orgarlisln wnichis not functional ly constrained tofeeding on one yeneral type of plantor animal but may feed on diverseprey from several trophic levels.Flocculation - Aggregation of small suspendedparticles due to ionicchanges brouyht on by contact withseawater.Fluviatile - Belonging to a river orproduced Dy river action (An. Geol .inst. 1976).Flow Ratio - Ratio of volume of uplandwater entering the estuary during atidal cycle to its tidal prism.

Fluvial - Of, or pertaining to, rivers. Obligate (Feeder) - Organism const rainedby moryholoyy or behavior to feedingFood Web - The pattern and sequence of on one general type of plant orfeeding interrelationships among theanimal.organisms of a community , from reducerand producer organisms to the Omnivore - Organism which feeds on bothhighest carnivores.plant and animal matter.Food Web Linkage - The trophic connectionbetween food web node.Food Web Module - Interacting species thatseem dependent upon specific prey resources,yi ve evidence for evolvedmodification for use of, or associationwith, these resources, and thatdisappear upon removal of a stronglyinteracting species {or appear withits addition) constitute a module(Paine 1980).Oliyohaline - Associated with head or lowsalinity, i.e., 0.5-5 lpt, reyion ofestuary (Symy. Class. Brack. Wat.1959).Pelayic - Characteristic of the water columnand not in association with thebottom.PhiUnits - Units of particle or grainsize where @I = -1092 dia (mm).Food Web Node - Species, taxon, or func- Planktivore - Organism which feeds ontional feeding group constituting asuspended zooplankton and nekton.unique prey or predator compartmentin a food web.Polyhal ine - Associated with middle andGravel - Hock fragments with diameters belowerreaches of estuary, typicallywith salinities between 18-30 ppttween 2 mm and 7.6 cm (Cowardin et (Symp. Class. Brack. Water 1959).al. 1979).Littoral - Pertaining to the shore zone Primary Production a ate) - ~easure ofbetween extreme high and low tide carbon fixed per unit area per unitlevels during spring tides. time by photosynthetic organisms(producers). usual ly expressed asMeropl ankton - Planktonic stages (eggs andy C m-2 hr'i.larvae) of organisms which in later1 ife wi 11 become members of the hen- Kheotaxis - Movement of an organism inthos or nekton.which a water stream or current isthe directive stimulus.Mesohaline - Associated with upper reachesor intermediate salinities, i.e., 5- Saline - Possessiny a hiyh deyree of sa-18 pyt, region of estuary (Symp. linity, i.e., more than 3°/00 (Am.Class. Brack. Mat. 1959). Geol. Inst. 1976).Nektonic - Capable of swirnrning againstnormal wave and current action,i .e., sel f-propel led.Neritic - Shallow surface water zone extendingfrom the high-tide mark tothe edye of the continental shelf.Neuston - Organisms associated with thesurface film of the water.Salinity - The total amount ot dissolvedsol id material (in grams) containedin one kilogram of water, expressedas O/, (ppt). For this measurementall organic matter is oxidized, allcarbonate converted to oxide, and allbromide and iodide replaced by chloride(Sverdrup et al. 1942; colloquial- the saltiness of a body ofwater).

Sand- Coarse-grai ned mineral sedimentswith diameters between 74 pm and2 mln (Cowardin et al. 1979).Spring Tides - The highest high and lowestlow tides during the lunar month.Standing crop - Term applied to biomass oforyanisms per unit area or volume.Standing stock - Term used to describecombined concept of density andstanding crop.Stone - Hock fragments with diameters between25.4 cm and 60.9 cm (Cowardinet al. 1979).Subaerial wet1 ands - Wetland habitatswhich lie between mean low water andmean high water.Sublittoral - Pertaining to the marinezone between extreme lowest 1 ow tidallevel and the margin of the continentalshelf.Subrounded - A roundness grade in whichconsiderable wear is evident, withedges and corners rounded to smoothcurves and the area of the originalfaces considerably reduced (An. Geol .Suspension feeder - Organism which processeswater for food, either passively(benthic) or actively (pelayic) entraining phytoplankton andother microscopic organisms and suspendeddetritus.Thigmotaxis - Movement of an organism inwhich contact with a solid body(i e., a1 gae, bottom sediments,rocks, pilings) is the directivestimulis; also called stereotaxis.Tidal amplification (factor) - Local tidalrange as a function (divided by) thetidal range at or near the mouth ofthe estuary.Trophic - Related to food, feeding, andnutrition.Trophic level - A group of oryanisms in afood web that secures food in thesame general manner.Volatile solids - Products, exclusive ofmoisture, given off as gas and vaporas determined by definite prescribedmethod01 ogy ; measure of organiccontent.

APPENDIX I3Sedinent Classification Schtmcs

Appendix fable 0-1. Various schemes of unconsolidated sediment particleclassification (Source: U.S. Army Corps Engineers 1973).Wentworth Scale(size description)PhiUnitsd*GrainDiameterd (mm)U.S.StandardSieveSizeUnifiedSoi 1Classification(USC)Bou 1 derCobble- 8256.0Cobble

APPENDIX CTidal Channel Characteristics Measurements(from Levy and Northcote 1981)

Measured Tidal Channel (TC) Characteristics1. TC mouth width (m)2. Width of TC at sampling station ( m)3. Distance from sampling site to mouth of TC (m)4. TC depth (m)5. Trough depth (cm)6. TC length (m)7. Average sedge height (m)8. Average szdiment particle size (microns)9. Distance to nearest subtidal refuge (m)10. Angular deflection to prevailing flowing tide (degrees)II. Channel order12. Sub- channel length (m)13. Angle of sedge bank (degrees)14. Slope of the tidal change (m/hr)15. Height of the high tide (m)16, Turbidity of the water at low tide (NTU)17. Area of the TC (m2)18. Compass heading of main axis of TC (degrees)19. Relative elevation of TC bottom (m)20. Elevation of surrounding bank (m)2 1 . Area of refugia at low tide (m2)22. Length of time TC submerged (hr )cross-sectionA1.LSLOUGH

Measurement of Tidal Channel tlabi tat CharacteristicsFish catch results from the May 10-17 surveys were comparedstatistically with habitat characteristics of tidal channels to assess hichcharacteristics were associated with high numbers of fish in different tidalchannels. The characteristics used in the analysis were chosen to be easilymeasurable either directly at the sampling site or in the laboratory, orindirectly from Fraser River Delta Project Maps. Figure 5 shows several ofthe tidal channel characteristics and Table 13 supplies numerical values.The fol lowing measurements were taken and included in statistical analyses:1. Width of the tidal channel mouth in meters (MTHWDTH) - measured inthe field from one tidal channel bank to the other perpendicular tothe axis of the channel.2. Width at the sampling site in meters (STNWDTH) - measured in thefield from one tidal channel bank to the other perpendicular to theaxis of the channel.3. Distance from the sampling site to the tidal channel mouth in meters(MTHDIST) - measured with a map measure from the Fraser River DeltaSeries Maps.4. Tidal channel depth in metres (CHNDPTH) - measured in the field atlow tide. A rope was stretched between the stakes at the level ofthe bank and a 3-meter pole, graduated at 5 cm intervals, waspositioned vertically in the deepest part of the tidal channel. Theheight at which the rope bisected the pole was recorded as thetidal channel depth.5. Trough depth in centimeters (TRODPTH) - the residual tidal f l o ~ nearlow tide frequently scoured a trough in the bottom of the tidal,channel which varied in depth between sampling sites.This depth was measured with a ruler during periods of low slacktide between June 7-13, 1979.6. Length of the tidal channel in ~neters (TCLNGTH) - measured witha map measure from the Fraser River Delta Series Maps. Thelength was defined from the position of the sampling site to thefurthest point on the 0 foot geodetic perimeter of the tidalchannel.7. Height of surrounding niarsh plants in ineters (IITSEDCC) -measured in the field during a one week period at the beginningof June, 1979 using a 3-meter pole graduated in 5 cnl intervals.

8. Mean sediment particle size (SFDSIZE) - replicate sediment sampleswere obtained on June 12, 1973 at all 18 tidal channel samplingsites. Samples of the upper 1 cm of sediment were collected with atrowel close to the center trough of the tidal channels andtransported to the Geochemistry Lab, U.B.C., in Whirl Pak Bags. Thesamples were dried in an oven in drying bags and then broken up witha mortar and pestlc. Individual samples were then placed on theuppermost (coarsest) of a series of 6 sieves and shaken for 5minutes. The fractions of sediment were weighed and the proportionof sediment in a given size range calculated as a fraction of thetotal sample weight. The average particle size in a given fractionwas asst~med to be half-way between the surrounding sieve sizes. Theproportion of sediment in a given fraction was multiplied by theaverage particle size to obtain weighted proportions of sedimentwhich were then summed to give an estimate of the mean particlesize. The average value of 2 replicates was used in the statisticalanalyses and is shown in Table 13.9. Distance to nearest sub-tidal refuge in meters (REFDIST) -determined as the distance from the sampling site to the nearestslough (sub-tidal) habitat capable of maintaining juvenile salmon at1 ow tide when no water occurred in the tidal channels. Thisdistance was measured off Fraser River Delta Maps with a mapmeasure.10. Angular deflection to prevailing flowing tide in degrees(ANGDEFL) - the angle of the axis of the tidal channel at the mouthto the direction of the flooding tide in the slough (Figure 5) wasmeasured off the Fraser River Delta Maps with a protractor.11. Tidal channel order (TCORDER) - tidal channels were classifiedaccording to the following characteristics:ORDERCHARACTER I ST I CS1 large sub-tidal slough or reach which never dewatersat low tide.2 large channel which experiences high velocity tidalflows and usually does not dewater at low tide.3 inter-tidal channel which branches off a 2nd orderchannel or slough and usually dewaters completcly atlow tide.small inter-tidal channel hich branches off a 2ndor 3rd order channel and always dewaters at low tide.

12. Total sub-channel length in rneters (SUBCHNL) - the length of a1 ltributaries flowing into the tidal channels was measured with a napmeasure. Only those tributaries deeper than the 0-foot contour wereincl uded.13. Average angle of the sedge bank in degrees (ANGBANK) - determined inthe field indirectly through measurement of parameter: A, B and C(shown on Figure 5) and calculation of angles r* and o( wl~ere o(=tan'l A/B and d = tdn-' A/C. The mean value for these 2angles was used to give a measure of the relative slope of the tidalchannel banks.14. Slope of the tidal change in meters per hour (TIDSLOP) - thedifference between the height of the predicted high and 10v~ tides atPoint Atkinscn was divided by the length of time between these twotides to give a measure of the rate of tidal flow for the datessampl i ng took place.15. Height of the high tide in meters (HTHTIDE) - the predicted levelsof the high tide at Point Atkinson for the dates sampling took placewere obtained from tide tables.16. Turbidity of the trough water at low tide in nephelometric turbidityunits (WATURB) - water sampling took place at low tide on June 12,1979 at a1 1 18 tidal channel sampling sites. Sub-surface sampleswere obtained from the trough of the tidal channel in 250 m1 plasticsample jars. Care was taken to avoid disturbing the sedimentupstream of the sampling site. Turbidity levels were laterdetermined in the laboratory with a tlach Turbidimeter.17. Area of the tidal channel in square meters (TCARCA) - measured byplanimetry from the Fraser River Delta Series maps. The margitis ofthe tidal channels were defined by the 0-foot geodetic contour.18. Compass heading of the main axis of the tidal channel in degrees(COMPASS) - the main axis of the tidal channel was drawn onto FraserRiver Delta maps and the difference between this line and theNorth axis was measured with a protractor.19. Elevation of the tidal channel bottom in meters (TCELEV) - the depthof water in the tidal channels was measured with a 3-meter graduatedstaff gauge at all eighteen sites over a 40 minute period near hightide on June 14, 1979. The location of the deepest part of thechannel was marked with a previously deposited anchor and float.Since all measurements were conducted at a time when the water levelwas static, measured differences reflected variations in bottom

elevation. The measured water depths were subtracted froin the levelof the predicted high tide at Point Atkinson to give a measure ofthe absolute elevation of the tidal channel bottom. Themeasurements were repeatl?d on two consecutive high tides to compareresults. Since the relative ranking of bottom elevation wasconsistent, only the June 14 results are shown in Tahle 13.20. Elevation of the surrounding bank in meters (BNKELEV) - the averageof two spot heights nearest the sampling site was determined fromthe Fraser River Celta Series maps. This served to give a measureof the absolute elevation of the surrounding marsh habitat above 0foot geodetic elevation.21. Area of low elevation refuges in square meters (AREAREF) - the areaof sub-tidal pools in the tidal channels bras planimetered fram theFraser River Delta Series maps. These areas were bounded by dashedlines and indicated low elevation depressions in the tidal channelswhich contained water at low tide.22. Time of submergence prior to sampling in hours (TIMESUB) -calculated by plotting tidal curves (predicted tide height at PointAtkinson vs. time) and defining the period of tidal channelsubmergence prior to sampling based on the measured tidal channelbottom elevations (no. 19 on p. 13). The number of hours at whichthe predicted tide level was greater than the measured elevationswas extrapolated off the tidal curves.

Appendix Table C-1. Measured tidal channel habitat characteristics. For explanation of terms and tinits ofmeasurement, see text.TldalSAWPLlNG SITESChannel Woodward Island Barber I s l end Lsdner Marsh Robsrts Be*Chwecterlst lcsW 1 Y2 W3 W4 W5 W6 81 82 83 84 85 Dl D2 03 04 05 FI F2MlHWDM 17.0 29.0 135 4.5 14.5 21.5 15.0 130 10.5 115 6.0 13.0 195 9.5 11.5 115 10.5 5.5STNWDTH 9.9 28.0 12.9 7.9 8.3 12.1 11.8 10.8 11.3 12.3 3.9 9.7 11.6 6.9 8.7 0 4 7.2 7.7MmD IST 192 53 85 30 35 1128 55 65 165 132 4 9 282 28 90 98 40 65CWTH 1.75 I 1.38 1.19 174 3 1 1-69 I.% 1.68 213 1-51 2-16 2.05 1.90 1.77 2.27 1.18 1.88lRODPTH 9.0 15.0 5.0 5.0 6.0 5.0 6.5 3.5 17.5 8.0 3.0 6.0 145 7.0 9.0 24.5 6.0 6.0TCLMiTH 495 870 480 391 566 234 352 370 891 315 346 770 463 215 376 480 414 533HT SEDGE 0.95 1-05 1.10 1.15 0.s 1.05 0.85 0.82, 0.96 O.R 0.90 1.10 1.0 0.95 1.35 1.40 o.n 0.60SEOS I ZE 192 I08 98 75 155 89 79 83 77 105 87 72 96 84 100 80 80 143REFDl ST 219 63 489 522 45 1143 70 189 108 216 1U 11 291 49 217 228 416 290ANGDEFL 79 56 57 57 46 57 % 79 20 78 65 102 31 111 0 0 60 77TCQIDER 3 2 3 3 3 2 3 3 3 3 4 3 3 3 3 2 3 3SUBCHNL 474 2210 838 31 1 476 492 659 N I229 495 75 200 495 78 252 221 983 4%ANOBAK 19.4 8.6 12.5 17.0 263 12.6 16.3 20.2 164 19.8 38.8 24.1 24.2 29-0 22.5 13.4 19.0 26.8" TIOSLW 0.44 0.44 0.44 0.44 0.44 0.44 0.49 0.49 0.49 0.49 0.49 0.48 0.48 0.48 0-48 0.48 0.46 0.46May 10-13T lOSL6 0.49 0.49 0.49 0.49 0.49 0.49 0.X 0.36 0.36 0.36 0.36 00.4 0.44 0.44 0.44 0.44 0.49 0.49Mey 14-17HTHT l DE 4.2 4.2 4.2 4.2 4.2 4.2 4.1 4.1 4 1 4.1 4.1 4.1 4.1 4.1 4.1 4.1 4.2 4.2May 10-13HTHT l C€ 4.1 4.1 4.1 4.1 4.1 4 1 3.7 3.7 3.7 3.7 3.7 1.9 3.9 3.9 3.9 3.9 4.1 4.1Way 14-17WATURB 110 77 2s 50 1 130 160 22 100 120 52 67 46 23 36 76 80 57TCAREA 4608 24071 6197 U)84 4097 2778 3855 4x15 9950 4311 1laO 393 2694 2044 2323 8240 4617 3214WASS 197 95 103 99 263 121 40 114 85 328 122 8 84 143 33 79 144 266TCELEV 1.6 1.41 1-95 2.09 1-68 2.19 1.67 1.91 1.62 1-66 1-96 1.81 1 2.12 1.94 1.58 2-34 2.21WKELE V 0.2 0.3 0.2 0.3 0.4 0.6 0.6 0.8 0.9 0.5 1.1 0.9 1.2 0.9 1.0 1.2 0.0 0.6AREAREF 37 2183 632 74 74 9 46 0 1623 37 0 0 46 56 0 1208 418 0T I MSUB 17.43 17.67 16.49 16.10 17.24 15.83 16.02 15.55 16.12 16.00 15.45 15.86 15.76 15.22 15.59 16.34 15.02 15.32Mey 10-13T IKSVB 15.75 16.13 15.12 14.86 15.62 14.68 1605 15.57 15.15 15.51 16.21 15.56 15-46 14-96 15-31 16.00 14.47 14.71Mey 14-17

APPENOIX DSumnary of Current Research andResearch Groups/Centers AddressingEstuarine Channel Ecology orEffects of A1 teration of Channel Habitats

Estuarine Channel Research in Pacific NorthwestOrganization:Oregon Institute of Marine BiologyUni vers i ty of OregonAddress:Contact(s) :Oregon Insti tute of Marine BiologyUni versi ty of OreaonCharleston, Oregon 97420Daniel Varoujean, Paul Rudy Jr.Type of Research : general es tuari ne ecologyLocation :Coos Baygrganizatiun: Oregon Department of Fish and Wild? ifeAddress: Oregon Department of Fish and Wild1 ifeOregon State Universi tyExtension Hal 1 303Corval 1 is , Oregon 97331Contact(s):Daniel Bottom, James Lichatowich, Kim Jones, Peggy HerringType of Research:estuarine utilization by juvenile salmonidsLocation: Oregon coastal estuaries , Coos BayOrganization:Department of Botany and Plant PathologyOregon State Uni vers i t yAddress:Department of Botany and Plant PathologyOregon State UniversityCorvallis, Oregon 97331Contact(s): C. David McIntireType of Research: benthic primary production; eelgrass production andphysiology; structure and production of epiphytic algaeLocation(s):Columbia River estuary; Netarts Bay

Organization: Department of General ScienceOregon State UniversityAddress : Department of General Science and, Marine Science CenterOregon State University Newport, Oregon 97365Corval 7 is, Oregon 97331Contact(s) : Robert Worrest,Dani 1 HancockType of Research: ecology of estuarine diatomsLocation:Yaqui na BayOrganization: Department of GeographyOregon State UniversityAddress : Department of OceanographyOregon State UniversityCorval 1 is, Oregon 97331Contact(s) : Robert Frenkel , Theodore BossType of Research:sal tmarsh comuni ty ecology; introduced species of estuarinemacrophytesLocation:Siuslaw River estuaryOrganization: School of OceanographyOregon State UniversityAddress : School of Oceanography and, Marine Science CenterOregon State University Newport, Oregon 97365Corvall is, OregonContact(s): Lawrence Small, Charles Miller, Robert Hol ton, Jefferson GonorJames GoodType of Research: water column primary production; phytoplanktonassemblage structure; zooplankton grazing onestuarine phytoplankton; pelagic zooplanktonassemblage structure and dynamics; benthicinfauna assemblage distribution and structureLocation (s):Columbia River estuary, Yaquina Bay, Coos Bay

Organization:Hammond LaboratoryNational Marine Fisheries ServiceAddress : Hammond LaboratoryNational Marine Fisheries ServiceP.O. Box 155Hammond, Oregon 971 21Contact(s) :Robert McConnell , George McCabe, Robert EmmettType of Research:fisheries ecology; distribution, abundance, and food habits ofjuvenile salmonids and Dungeness crabLoca ti on :Columbia River estuaryOrganization:Battelle Marine Research LaboratoryBattelle Memorial Institute NorthwestAddress : Battel le Marine Research Laboratory439 West Sequim Bay RoadSeqbim, Washington 98382Contact(s) : James Young, Walter Pearson, Jack Anderson, Charles GibsonType of Research:estuarine ecology of benthic infauna, pelagic zooplanktonand f.ishes; effects of oil pollution on estuarine communitiesLocation :Strait of Juan de Fuca and northern Puget SoundBrganization: Fisheries Research Insti tuteUniversity of Washington .Address: Fisheries Research Institute WH-10College of Ocean and Fishery SciencesUniversity of WashingtonSeattle, Washington 98195Contact(S): Charles Simenstad, Robert Wissmar, Ernest Salo, Quentin Stober,Bruce MillerType of Research: estuarine utilization by juvenile salmonids; food webstructure of Pacific Northwest estuaries; structureand dynamics of epi benthic and neri tic zooplanktoncomnuni ties in estuaries; estuarine fish assemblagestructureLocation :Hood Cana 1, Puget Sound and component estuaries , Grays Harbor,Columbia River estuary

Organization: School of FisheriesUniversity of WashingtonAddress : School of Fisheries WH-10Col lege of Ocean and Fishery SciencesUniversity of WashingtonSeattle, Washington 98195Contact(s) : David Armstrong, Kenneth Chew, Ronald Thorn, Jack WordType of Research:basic biology and ecology of estuarine crustaceansand molluscs; early life history (larval) of economical IYimportant crustaceans; maricul ture of estuarine organi SmsLocation :Grays Harbor, Puget Sound and associated estuariesOrganization: Department of OceanographyUniversity of WashingtonAddress: School of Oceanography WE-10Col 1 ege of Ocean and Fisheries SciencesUniversity of WashingtonSeattle, Washington 98195Contact(s) : Joe Creager, Chris Sherwood, David Jay, T. Saunders Engl i sh,Peter Jumars, Arthur Nowel 1Type of Research: estuarine sedimentology and circulation; estuarine zooplanktonand larval fish distribution, abundance, andecology; benthic infauna and epi fauna ecologyLocation: Columbia River estuary, Puget Sound and associated estuari esOrganization: Huxley College of Environmental StudiesWestern Washington UniversityAddress : Huxley College of Environmental StudiesWestern Washington UniversityBe1 1 i ngham, Washington 98225Contact(s) : Wi 11 jam Summers, Bert WebberType of Research:ecolow of estuarine and nearshore marine algae andbenthic. invertebrate comuni tiesLocation: northern Puget Sound estuaries

Organization : Department of OceanographyUniversity of British ColumbiaAddress : Department of OceanographyUniversity of British ColumbiaVancouver, British Columbia V6T 281CanadaContact(s) : Brenda HarrisonType of Research:Location: Fraser Ri ver estuaryecology of estuarine benthic and epibenthic invertebratecomnuni ti esOrganization: Department of BotanyUniversity of British ColumbiaAddress: Department of BotanyUniversity of British ColumbiaVancouver, Britich Columbia V6T 2B1CanadaContact(s) : Paul Harrison, Richard BigleyType of Research : seagrass (Zos tera spp. ) cormuni ty ecologyLocation:Strait of Georgia estuaries, northern Puget SoundOrganization : Wes twa ter Research CentreUniversity of British ColumbiaAddress: Westwater Research CentreUniversity of British ColumbiaVancouver, British Columbia V6T 1W5CanadaContact(s) : Thomas Northcote, David Levy, Anthony Dorcey, Kenneth Ha1 1Type of Research:estuarine utilization by juvenile salmonids; managementof estuarine habitats; effects of log rafting, dikingand filling, and construction of training wallsLocation:Fraser River estuary

Organization : Department of Biological SciencesSimon Fraser UniversityAddress:Contact (s):Department of Biological SciencesSimon Fraser Un iverst iyBurnaby, British Columbia V5A 1S6CanadaMichael St anhopeType of Research:estuarine ecology of gammarid amphipods with referenceto log storage effectsLocation:Squami sh and Fraser River estuariesOrganization:Address:Contact(s):Fisheries Research Branch,Salmon Habitat Research Sect ionl~est Vancouver Laboratory,z~acif ic Biological Stat ion,4160 Marin eDrive, Departure Bay Road.West Vancouver, B.C. V7V IN6 Nanaimo, R.C. V9R 5K6Canada9Colin ~evin~sl, Mich el ~aldichukl Me1 ~ o t ~ k lT.J. ~rown~, B. Kask , I. ~irtwelyl, G. ~reer~.C. MCA~1 ister2,Type of Research:Locat ion:ecology of gammarid amphipods in estuarine habitats; feedingecology of juvenile salmonids; survivorship of chinookreleased in estuarine and alternate habitats; effects ofdomestic waste on juvenile salmonids in estuariesFraser River, Campbell River, Nanaimo River estuariesOrganization: Pacific Biological StationAddress: Pacific Biological StationDepartment of the EnvironmentP.O. Drawer 100Nanairno, British Columbia V9R 5K6CanadaContact(s) : John Sibert, Robin LeBrasseur, Michael Healey, Brent HargreavesType of Research:estuarine utilization by juvenile salmonids; ecology ofepibenthic zooplankton; estuarine feeding ecology of juve~ilefishesLoca ti on :Nanairno River estuary, other Vancouver Island estuaries

--50272 -101'REPORTPAGE-- --4. Title and SubtntleTHE ECOLOGY OFA COMMUNITY PROFILE ---- -- - - - - - - - - -- -9. Performing Organlzatlon Name and AddressFisheries Research InstituteCollege of Ocean and Fishery SciencesUniversity of WashingtonSeattle, WA 98195- -3. Rectplent's Accession No- ---- -8. Perform~ng Organlzatlon Rep:. No.I- . - -- -10. Pro~ectlTaskIWork Unit No1.- . -11. Contract(C) or Grant(G) No.--- -- -.-- -- ---- --- -- --p Organ~zatton Name and AddressFish and Wild1 ife ServiceDivision of Biological Services--- - --U.S. Department of the Interior li4 ' --Washington, DC 20240- -IS. Supplementary Notes--16. Abstract (Ltrnlt: 200 word$)This report on the estuarine channel habitats of the Pacific Northwest is one of a series ofcommunity profiles that synthesize useful information about specific natural coastal habitats.This profile will assist environmental scientists and biologists and coastal plannersand managers who are interested in the open-water channels of coastal estuaries from theStraits of Juan de Fuca in Washington, south to Cape Mendocino, California.The profile describes the geomorphological , hvdrological , chemical, and biological componentsand natural processes of the channels, their energy interchange, and interactionsamong adjacent habitats. In combination these habitat components and their interactionsdictate the ecological structures and functions of the channels. The subject materials ofthe various chapters are integrated and summarized in the last chapter, and considerationsfor habitat management are identified.117. Oocument Analysis a. Oescriptors1ChannelsHydro1 ogyEcologyPacific NorthwestEstuariesb Identlflers/Open Ended Terms_, __._______I__.^_ _ _- _ _ __ . _ --c COSATI F8eldIGroup-18. Avatlab~laty Statement ; 19. Securtty Class (Ths Reporf)(See ANSI-239.18;Unl imi ted ! . ~ ] fieh-- ~ ~ jUnclassified120. Secur~ty Class (Ths Page) 22. PrjceIOPTIONAL FORM 272 (4-77)(Formeriv NTIS-35)Department ol Commerce* U.S. GOVERNMENT PRINTING OFFICE: 1984-772-308