Pájaro River Watershed Flood Protection Plan - The Pajaro River ...

California State University 

Robert Curry, Research Director 

Watershed Institute 

Earth Systems Science & Policy 

CSU Monterey Bay 

Seaside, CALIF. 93955 

Bob_curry@csumb.edu 

Watershed Restoration Class – Spring, 2003 

Pájaro River Watershed 

Flood Protection Plan 

Wm Bodensteiner 

Lani Clough 

Suzanne Gilmore 

Paul Huntington 

Joy Larson 

April McMillan 

Steve Mack 

C. Andrew Mauck 

Serena Pring 

Emily Roth 

Amy Thistle 

Melanie Vincent 

DRAFT OF July 22, 2003 A1 Public Copy

Executive Summary 

Because of the unique geologic and hydrologic setting of the Pájaro River in 

its dynamic watershed, traditional approaches to flood control may not be 

effective and will require constant expensive maintenance. The river that 

now flows through it did not create the lower Pájaro Valley and it is not 

possible to “restore” such a system to stability because there is no evidence 

of any past stable Pájaro River channel in the lower valley. An artificial flood 

control channel was constructed by early residents and was upgraded by the 

U.S. Army, and later by the Corps’ of Engineers to try to minimize property 

losses associated with large floods in this watershed of about 1300 square 

miles. Historically the Pájaro watershed system has carried runoff from 

Santa Clara, San Benito, Santa Cruz, and Monterey counties into Monterey 

Bay through various channels in Monterey County. The river is now 

artificially confined to join Corralitos Creek to enter the ocean along the Santa 

Cruz/Monterey County border. 

We find that a substantial area of on-channel storage of floodwater has been 

lost in the upper watershed areas of San Benito and Santa Clara counties. 

Some of this lost storage can be recovered for little or no public cost to 

reduce flood heights (on the order of 4 feet) in the artificial floodway channel 

of the lower river. Redesign of that lower channel may accommodate added 

flood capacity to provide a working flood channel that carries a generously 

estimated 100-year flood volume. Such redesign, coupled with upstream 

channel restoration that is part of a flood storage enhancement project, will 

have very substantial wildlife and water quality habitat benefits. 

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Pájaro Watershed Flood Management

Table of Contents 

Executive Summary 

Table of Contents 

Chapter 1 

Introductory Context 

The Pájaro Watershed System Dynamics 

The Watershed 

Lower Watershed – Santa Cruz and Monterey Counties 

Upper Watershed – San Benito and Santa Clara Counties 

The River System 

Stable Channel Alternatives 

This Project Report 

Coordination with other 

Raines, Melton, Carella 

Philip William Associates 

U. S. Army, Corps of Engineers 

i 

ii 

Chapter 2 

Design Flood Analyses 

Purpose 

Methods 

Data Collection 

Data Analysis 

Results 

Regional Analyses 

Discussion 

Storm Patterns and History 

Chapter 3 

Upper Basin In-channel Flood Storage and Restoration Opportunities 

Basic Conclusions 

Theory 

Methods 

Findings 

Channel Incision 

Channel Diversions 

Restoration of Channel Functions 

Suggested Restoration Options for the San Benito River 

Aggregate Mining Company Opportunities 

Suggested Enhancement Options for the Upper Pájaro River 

Conclusions 

References Cited and Historical Materials Consulted 

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FIGURES AND PLATES 

Fig 1 Map of Lower Pájaro River and Elkhorn areas showing historical changes 

Fig 2 Historical aerial photo of Pájaro Valley showing landslides 

Map A Rancho Vega del Rio Pájaro and Northern Monterey County 1875 

Map B Land Ownership in Vega area about 1910 

Fig 3 Historical (1938) aerial photo showing past breakout areas 

Fig 4 Historical (1938) aerial photo showing meander wavelength in lower valley 

Fig 5 Map of Pleistocene Lake San Benito (from Jenkins) 

Fig 6 Calculated flood discharge frequency/magnitude plot at Chittenden 

Fig 7 Monterey Herald photograph of 1938 Lower Pájaro flooding 

Map C FEMA 100-year flood map and map of areas considered for flood storage 

augmentation in this report 

Fig 8 Soil profile in active overbank storage areas 

Fig 9 Lake San Benito soil profile 

Fig 10 Example of area that can be restored to flood storage 

Fig 11 Effects of channel incision on channel stability and habitat 

Fig 12 Cienega Road House 

Fig 13 Llagas Creek Channel photos 

Fig 14 Gabion Basket representation 

Fig 15 Stream Barb representation with Gabion Baskets 

Fig 16 Detailed topography of a portion of Lower San Benito River near Highway 101 

Fig 17 San Benito River Channel topography near Mitchell Road 

APPENDICES 

App 1. Note on higher recorded 1998 flow at Highway 156 than downstream at 

Chittenden gauge from L. Freeman, USGS 

App 2. Analysis of 1998 and 1995 storm conditions with map of precipitation stations 

used in the analysis 

App 3. Streambank property owners in San Benito County (separate file) 

App 4. In preparation 

App 5. Example of Historical Changes in Lower San Benito River (Figs 18-21) 

App 6. Topographic detail for a cross section in the App 5. Historical Change area 

App 7. Mines in the San Benito County permit files (separate file) 

App 8. Economics and Socioeconomic Settings 

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Pájaro River Watershed Flood 

Management Alternatives 

A study by the CSUMB Watershed 

Restoration Class, Spring 2003 

CHAPTER 1 

Introductory Context 

This report is a group effort of 12 upper level students who have focused much of their 

education on Watershed Science through the Earth Systems Science and Policy 

Program at California State University Monterey Bay. Some participants had already 

graduated from CSUMB or UC Santa Cruz; while most were finishing seniors with 

educations that included advanced hydrology, water law, and riparian ecology. CSU 

Monterey Bay stresses an “outcomes-based” education with active, applied learning. 

This work is not financially supported, but a small anonymous donation of $500 

helped with copying and telephone costs. The Santa Clara Valley group “People for 

Livable and Affordable Neighborhoods” supported a detailed watershed map made 

especially for this effort by Eureka Cartography in Berkeley. San Benito County and 

the Graniterock Company contributed map and data resources. 

This report follows the theme of our educational program and treats the Pájaro 

Watershed as a physical and biological system. We take the position that it is not 

possible to isolate the processes and problems in the lower watershed from the 

causal mechanisms in the upper watershed. We look at the watershed as a complete 

system with material and energy flows that support living ecosystems and organisms. 

We assess the causes of dysfunction, which in this particular case focuses on 

responses of humans to flooding and sediment transport, and evaluate potential 

solutions utilizing fundamentals of fluvial geomorphology and restoration ecology. 

This particular study was undertaken in the context of significant fundamental 

disagreements between residents, agencies, and government entities. Following the 

California Supreme Court finding that upheld lower court’s rulings against County 

governments for causing flooding in 1995 through lack of required maintenance, 

Monterey and Santa Cruz counties requested that the U.S. Army Corps of Engineers 

consider a new flood control project to protect the downstream areas from 100-year 

return-period floods. This class effort focused on the opportunities to reduce 

downstream flood hazards through upstream flood detention and through design of a 

stable channel alternative in the artificially constrained lower reaches of what is called 

the Pájaro Valley. 

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The Corps’ had been requested to evaluate protection options for only the lower river 

system working with only the lower county governments, and further constrained by 

limited budgets and the necessity to work with a set of “stakeholders” who 

represented diverse and often contradictory viewpoints. With this impossible set of 

constraints, landowner, environmental, and agency views that had seemed in conflict 

with each other soon refocused on conflict with the Corps’ themselves, who ultimately 

were left to represent only the county governments who had brought them into the 

project. 

This report is now presented simultaneously with the Corps of Engineers flood control 

proposals and with a citizens’ sponsored and funded set of alternative flood protection 

solutions produced by the renown hydrologic consulting firm of Philip Williams 

Associates. It is hoped that this university effort can help to expand the very limited 

scope of the many other ongoing and recent studies to create viable alternatives in 

this very complex watershed system. 

The Pájaro Watershed System Dynamics 

The Watershed: At present the Pájaro River watershed drains an area of 

approximately 1300 square miles. The watershed primarily drains the counties of San 

Benito, and Santa Clara, with some added contribution from Santa Cruz County. Very 

small areas of Fresno and Monterey counties are also within the watershed but 

contribute very little to the runoff. About 91 percent of the watershed is in North 

America while the outlet in the Lower Pájaro Valley and the Corralitos and 

Watsonville Slough tributaries are on the Pacific Plate. Due to active faulting within the 

watershed boundaries, the rivers’ coarse is continuously changing and has not 

stabilized in a valley of its own construction. The San Benito River is now 51% of the 

entire Pájaro drainage area but contributes only about 25% of the runoff at Chittenden 

(an average of 49 ac-ft/an/sq.mi.) The Pájaro above the San Benito junction (at 

Sargent) contributes about 180 ac-ft/an/sq.mi from 39% of the basin. 

Corralitos/Salsipuedes tributary is only about 3% of the watershed but contributes on 

the order of 435 ac-ft/sq.mi, or nearly 10% of the total discharge of the Pájaro system. 

Constructed reservoirs have a maximum capacity of 42,680 ac-ft (Hernandez:18,500; 

Uvas:9950; Chesbro:8090; and Pacheco:6140). We estimate that about 60,000 ac-ft 

of near-channel flood storage also exists in areas that are subject to overbank or inchannel 

flood storage or were 50 years ago. About 24,000 ac-ft of lost storage can be 

readily restored at little or no public cost. 

A map of the watershed that incorporates the detailed findings of this report is 

available on-line in a medium-resolution 10 MB and low resolution 700 KB version at 

http://home.csumb.edu/c/currybob/world/Pajaro/ where this report itself and some of 

its graphics is also available. This watershed map utilizes the existing left-bank levee 

of the lower river as the watershed divide between Elkhorn Slough and the Pájaro 

watersheds. 

Lower Watershed, Santa Cruz and Monterey Counties: The Pájaro Watershed is 

unusual. Traditional engineering solutions must accommodate the unique geology and 

hydrologic character of the basin. The headwaters of the basin are in North America 

but the primary plate boundary represented by the Calavaras and San Andreas Fault 

zones separates the mouth of the present river from its historic source areas. Active 

transform faulting has repeatedly and progressively modified the course of the river 

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that today bears the name Pájaro. The unusual shape of the watershed itself, with a 

long source area far south of the outlet is the result of continual stretching of the 

watershed by active faulting that pulls the lower river northwestward, farther and 

farther from its headwaters. 

Much of the lower river, west of the San Andreas Fault Zone, does not flow in a valley 

of its own making. The original course of Corralitos Creek in Santa Cruz County (see 

Fig. 1) and its alluvial aquifer have now been taken over by the Pájaro River system. 

The ancestral Pájaro River has been repeatedly offset northward by right-lateral fault 

offset, sometimes emptying to the coast through Elkhorn Slough at Moss Landing, 

and other times commingling with Corralitos Creek as it does today. California’s State 

Geologist, Olaf Jenkins (1973) postulated that landslides near Chittenden Gap, 

forming Lake San Benito and later Lake San Juan that repeatedly spilled and scoured 

overflow channels in the Carneros Creek/Elkhorn Slough area, might have repeatedly 

dammed the main river. Even today, during flood stage, the lower river flows to the 

sea at Moss Landing. Jenkins reasoned that these changes are geologically 

contemporary, having occurred in the last few thousand to 20,000 years at the most. 

Fundamental evidence for the very young character of this lake and its overflow is the 

fact that the lake shorelines are evidently not evidently tilted or deformed, despite 

being astride two active faults, and finding that the lake sediments contain a fully 

contemporary local flora and fauna. 

Fig 1 

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Figure 1 represents a slight modification of the original Jenkins map (Curry, 1996) with 

a series of name changes to better reflect the geologic evolution of the present lower 

Pájaro River as it spilled through Chittenden Gap to overwhelm any preexisting local 

watercourses. It is critical to appreciate that Corralitos Creek and its presumed 

tributary Aromas Creek did not capture the Pájaro River, but instead a great lake 

dammed by faulting and/or landslides spilled catastrophically into what we now call 

the Pájaro Valley. This explains the lack of terraces and floodplain deposits in the 

lower Pájaro Valley, and the massive Lake San Benito silts that now blanket the lower 

valley to support its agriculture. 

Because the river that now flows through it did not form the lower Pájaro Valley, the 

watercourse is inherently unstable. Fluvial geomorphology recognizes this condition 

as “overfit”, with the natural watercourse being too big for its channel. Coupled to this 

inherent instability is the fact that the lower Pájaro Valley is traversed by the San 

Andreas Fault and the subsidiary Zayante-Vergeles fault system (R. Anderson, 1990). 

These are all among the most active terrestrial fault systems on the North American 

continent. The 1989 Loma Prieta earthquake apparently deformed the Pájaro River 

levee system (personal survey notes). Today the lowest point in the Pájaro Valley is 

not the Pájaro River but is a small overflow watercourse along the extreme south side 

of the lower valley. Based on undercutting of the hillsides at the south edge of the 

present Pájaro Valley and preserved cutoff meanders there, the southernmost edge of 

the valley has been the lowest point for at least several hundred to several thousand 

years (see Fig. 2). 

It is thus perplexing that the present river course and levee system coincide with the 

lower Corralitos Creek channel. Based on the early maps made shortly after 

statehood in 1850 and local place names, a grazing wetland commons existed in the 

Mexican Ranchero period in the area still known as the Vega (see Map A, Rancho 

Vega del Rio Pájaro, Map B). The vega meadows here were apparently flood irrigated 

regularly to constrain land use and thus provided a grazing Mexican land grant until 

Statehood and private (Porter) ownership. The Vega is adjacent to a spot on the 

original river (see Map A) where the river was straightened after the boundary 

between Santa Cruz and Monterey counties was established (California Historical 

Survey, 1923). An alluvial thalweg (central river channel) is now buried beneath the 

levee system and has been the locus of flood outbreaks from at least the 1930s 

through 1995 (see Fig 3). All of the positions of today’s levees crossing the 1854 

channel position are sites of piping and passage of river water under the levees during 

high water as seen in 1995 and 1998 (personal observation, R. Curry and landowner 

discussions). 

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Map B. 1908 Parcel Map of a portion of the Lower Pájaro Valley showing the historic 

Vega area and dot-dashed County boundary as it exists today. 

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Figure 2 -- 1939 Photo of Lower Pájaro Valley. Watsonville in lower right. The 

landslides are readily seen at the position of Highway 1 today, near the center left of 

the photo. Also visible are the flow lines from past floods that impinge against the left 

(south) side of the valley. 

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Map A 1875 based on 1854 land survey 

It may be that in the Ranchero and early statehood period, the lower Pájaro River was 

channelized to try to restrict regular overbank flow in distributary channels so that land 

use could be made more efficient. Looking at the 1939 and earlier aerial photos, we 

still see clear evidence of those distributaries (cf Fig. 3). The earliest detailed 

topographic map (Capitola Quadrangle, 1912) shows “Watsonville Creek” that flows 

from the left bank of the Pájaro River across that river from Salsipuedes Creek in 

Watsonville, directly south near Salinas Road and into Elkhorn Slough. That channel 

is still there and still carries rainfall and flood overflow runoff to Moss Landing. Runoff 

from a major part of the townsite of Pájaro does not enter the Pájaro River today but 

flows via “Watsonville Creek” to Elkhorn Slough. The confusing topography was 

commented on by William Brewer in his diary in 1864 that noted that the flat valley 

looked like "an old lake filled in as is shown by the terraces around its sides." 

(Farquhar, 1930). Olaf Jenkins identifies a “Lake Pájaro” and “Lake Aromitas” in the 

old lower Pájaro Valley (1973). 

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Figure 3 - 1938 Image of Lower Pájaro River showing natural meander patterns 

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Upper Watershed, San Benito and Santa Clara Counties: The upper watershed of the 

Pájaro system is at least as complex as that of the portion west of the San Andreas Fault. 

There is indirect geologic evidence that Santa Clara Valley from San Jose southward 

through Morgan Hill and Gilroy may have been the course of a major river carrying coarse 

gravels southward toward the present Pájaro River and that a lake in San Benito County 

later spilled northward along Coyote Valley into San Francisco Bay (Iwamura, 1995). An 

open and porous alluvial gravel characterizes the near surface substrate beneath both the 

north-flowing Coyote Creek and the south-flowing Llagas and Uvas Creek valleys. A very 

low gradient “watershed divide” near Morgan Hill has southward flow in a shallow 

subsurface aquifer, presumably recharged by Santa Clara Water District facilities from 

California Water Project sources (Anderson Reservoir) and from locally captured and 

diverted watercourses. Where this shallow gravel aquifer is exposed in the bank of the 

Pájaro River, along the westernmost Santa Clara -- San Benito County border, many 

cubic feet per second of water flow continuously into the Pájaro River. These high water 

tables were recognized long before the San Luis Project brought Mt. Shasta water into 

southern Santa Clara and northern San Benito counties. The high groundwater levels are 

recognized as a particular agricultural problem in San Benito County (Jones & Stokes, 

1998) where some are saline. 

The thick uniform silt deposits of Northern San Benito and Southern Santa Clara 

counties are themselves enigmatic (see Fig 5 from Jenkins). Jenkins refers to them 

as “Pleistocene” meaning of Pleistocene age (greater than 10,000 years ago) and 

draws parallels with glacial age origin silts. Indeed, the surface deposits of lakebed 

silts are remarkably uniform fine sandy silt similar to glacial origin rock flour in both 

texture and lack of chemical weathering. But calling upon an ancestral San Joaquin 

River system to deposit these silts from the Sierra Nevada is, at present, not 

demonstrated. Jenkins hypothesizes that the silts may be derived locally from the 

older Purisima Formation (locally now called the Etchegoin Formation east of the San 

Andreas Fault). Subsurface deposits of northern San Benito County are characterized 

by localized sands and gravels that appear to be river deposits embedded in silts 

formed in shallow ephemeral lakes (Stanley, et al, 2002; Jones & Stokes, 1998). 

These are then buried by the more uniform overlying silt lakebeds. It is these surface 

lake silt unit(s) that have been transported downstream to blanket the lower Pájaro 

River Valley. It is not clear that they are being eroded from agricultural fields 

upstream, and may simply be carried in flood flows from upstream bank erosion. 

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Figure 5 Jenkin’s map Lake San Benito with its tectonic setting 

The Calavaras, San Andreas, and Sargent fault zones define much of the course of 

the present tributaries of the upper Pájaro River system. These right-lateral strike-slip 

plate-bounding fault systems essentially lengthen the headwaters of the Pájaro River, 

repeatedly moving the upper river system southward 10’s of kilometers relative to the 

Pacific Plate. The Old San Juan Stage Road between Salinas and San Juan Bautista 

appears to follow an abandoned course of what is now called the San Benito River 

after that river was pulled northward on the west side of the faults to join the upper 

Pájaro River. All of this may have happened during as little as a few hundred or 

thousand year period of lakes being dammed and spilling before the river ultimately 

broke through the Chittenden water gap to spill westward rather than southward. It is 

interesting to note that this rare example of a true water gap in western United States 

is actually called “Chittenden Pass”. A water gap is a pass through a mountain range 

or ridge cut by water. These are generally found in places like the Appalachians 

where a very old river is able to keep flowing while mountains are arched upward 

beneath it or while erosion lowers the river across a buried bedrock feature. 

Chittenden Pass is indeed a narrow part of the new river valley but cut by 

catastrophically spilling water. 

The River System: No other reasonably large North American river drains a 

watershed that is as complex or as geologically active as the Pájaro . Only in the 

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Himalaya and Alaska are there possibly watersheds of greater than 1000 square 

miles with an equal level of active watercourse displacement and contemporary 

changes in drainage area, and those rely in part on glaciers to block and divert the 

faulted landscapes. The Pájaro is unique in that geologic activity must be factored in 

to an understanding of the dynamics of flood hazard evaluation in a populated area. 

Ongoing geologic deformation renders constructed features like levees and channels 

very impermanent. Stream gradients and streambed elevations are changing by feet 

per century from non-anthropogenic causes (cf, 1906 earthquake and loss of 

navigability of Elkhorn Slough to the commercial steamer carrying Watsonville cargo 

to Moss Landing, Loma Prieta earthquake, creep on the Calavaras fault). Traditional 

approaches to flood hazard mitigation must accommodate this constant change. 

Stable Channel Alternatives: Stable channel concepts are almost a tautology in a 

constantly changing watershed system. But because we have 65 year-old or older 

aerial photos of almost the entire watershed, we can find evidences of the 

characteristics of river channels and flood patterns preserved from the time before 

laser leveling and powerful tractors. Many of the historic areas of lowland flooding 

and lake silts throughout the watershed were initially farmed as orchards. Uplands 

were used for hay and barley. The lower Pájaro Valley was noted for its apples and 

the upper valleys for walnuts (Crosetti, 1993). These seasonal crops were tolerant of 

winter flooding, seasonal root saturation, and some aggradation. Access to farmlands 

with mechanized equipment and safety of grazing animals led to efforts to straighten 

channels and, as elsewhere in the world, to shorten channels and cut off meander 

loops. The 1854 Coast and Geodetic Survey mapping, later expanded in the 1870’s 

to include more inland areas through the U.S. Lands Office, showed that the Pájaro 

had been altered by the time of statehood. The 1854 survey, at a scale of 1:10,000, is 

accompanied by survey notes (Wm. M. Johnson, 1854) that state: “Extending from the 

mouth of the Pájaro River to the Salinas River is a range of low sand hills between 

which and the older formation lay several ponds. These mark the former bed of the 

Pájaro, it having evidently at one time, found its way to the ocean through this 

channel, but by an accumulation of its waters, during the winter months, it burst the 

narrow strip of beach which separates it from the sea, and thus formed itself a new 

more direct outlet”. By 1909, the Coast and Geodetic Survey report noted that the 

Pájaro River “has low but well-defined banks and there is no evidence of recent 

changes in its course” (1910 C&GS survey notes). Those coastal surveys generally 

extended only 2.5 miles inland. 

Maps of Santa Cruz and of Monterey Counties were prepared in the 1870’s and are 

on file in the University of California Santa Cruz map library (see list in References 

Cited). An example is shown as Map A. It is important to appreciate that the river 

plan form shown in these early commercial maps was based on earlier US Land 

Office plat maps and the Coast and Geodetic surveys. It is the County boundary 

maps that show accurately the changes in position of the Pájaro River and that must 

be used for the actual position of the river (California Historical Survey Commission, 

1923). Based on that definitive reference, the channel of the Pájaro had been 

straightened shortly after Statehood and continued to be altered through the late 

1800’s. 

Based on geomorphic understanding of the relationships between a river and its 

natural floodplain, one can establish a channel geometry that, for a given gradient and 

sediment load, can approximate the shape of a channel that is self-maintaining (Curry, 

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1981; Riley, 2003). Of course, the lower Pájaro River does not have a floodplain in 

the normal sense of a surface of deposition and transportation of sediment and water 

that exceeds the effective dominant discharge of the river system. The lower Pájaro 

Valley land surface is a flood-deposit, but not one formed through an equilibrium 

relationship between its river and its flood regime (see Whiting, 1998). Thus, use of 

standard hydrologic relationships between flood frequency and magnitude to estimate 

ideal channel dimensions and form may be limited in applicability. Not only is the river 

changing in length because of human channel shortening, but also the seaward limit 

of the river mouth has moved inland many 10’s of meters since the first 1854 survey 

(1910 C&GS survey notes). Further, tectonic deformation may be tilting the whole 

lower Pájaro Valley and surroundings southward. Still further, changed drainage 

areas in the upper watershed and incision of watercourses are apparently increasing 

the ratios of runoff to rainfall. 

But use of historic aerial photos to interpret pre-channelization or flood-time flow 

patterns can provide clues to the “natural” channel form that the Pájaro would take if 

unconstrained. As pointed out by outside Corps of Engineers project review team 

members (USCofE, 1998), the current levee-constrained channel may not reflect a 

stable channel configuration. British work, funded through the US Army Corps of 

Engineers, has concluded that, as a general rule in sand-bed rivers, the mean annual 

discharge and the bankfull discharge form lower and upper bounds, respectively, to 

the range of effective discharge, while the 2-year flow is an upper bound to the range 

of bankfull discharge (Soares, cite). 

Ron Copeland provided a contribution to the Corps’ Project Review Team report for 

the lower Pájaro Project (USCoE, 1998). He suggested that use of a channel-forming 

dominant discharge with a probability of recurrence of 1.5 to 2.0 years could permit 

estimation of ideal bankfull width and meander wavelength for a given gradient, 

roughness, and sediment load regime. That is the same approach as described by 

Rosgen in his Fig 1 (see next) (Rosgen, 1996). It has real merit. Copeland included 

Fig 4 from Akers and Charlton, 1970, in his contribution to the Pájaro review team 

report (figure follows). Using a calculated (Fig 6) discharge for a 2.0-year return 

period at Chittenden, we calculate that the dominant channel-forming flow that should 

equate to bankfull discharge in a stable channel is about 3500 cfs. Using that value in 

the Ackers and Charlton figure yields a stable meander wavelength for a channel 

unconstrained laterally by levees with a value of 1000 to 1500 feet. That is what we 

see in the historic overflow channels on the old aerial photos (Fig 4), and in the early 

historic maps of the river platform. Thus there is a corroboration of theory and 

systems function in the lower Pájaro River channel, despite the unusual nature of the 

relationships between the watershed and the areas subject to flooding. 

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99% = 1.010 yr 

95% = 1.053 yr 

50% = 2 yr 

5% = 20 yr 

1% = 100 yr 

0.2% = 500 yr 

100000 

10000 

Magnitude 

1000 

100 

Pajaro River at Chittenden 1940-2000 

10 

1 

-3 -2 -1 0 1 2 3 

Standard normal deviate of probability of excedance 

Figure 6: Plot of actual peak floods (X‘s) versus LogPearson Type III calculated 

values (open Circles). This is not calculated using the required methodology, as done 

in Chapter 2. 

This Project Report 

When the original U.S. Army Engineers flood control project was begun in 1943 and 

completed in 1948, all 4 counties in the watershed signed off on an agreement to 

accept responsibility for maintenance of the flood control works in accord with a 

detailed maintenance plan prepared by the Army (Secretary of War, 1944). In the 

1960’s the upstream counties, under the organization of Santa Clara County, 

requested a Congressional exemption from the earlier agreement (Secretary of the 

Army, 1965), and it was granted. This political context prevented several efforts to 

develop a watershed-based joint powers authority to manage the watershed after the 

March, 1995 floods that took one life in Pájaro and caused many millions of dollars of 

losses in the Lower Valley. 

Congressional efforts in response to landowner concerns following the 1995 and 1998 

floods lead to appropriations for, and efforts by the Corps’ to review and revise the 

flood control project. Because of the failures of prior efforts to solicit cooperation from 

upstream counties, it was deemed politically necessary to restrict the scope of flood 

control efforts to a downstream project that simply rebuilt the original 1948 project 

within the same reaches of the Lower Pájaro River that had been the subject of 

structural efforts in the past (Congressman Sam Farr, personal communication). 

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The current project attempts to rectify the inability of the government efforts to 

consider solutions that most effectively and economically deal with the river system 

rather than only the lower river reach. While this is a suitable context for investigation 

by an academic institution, it also provides a public service outside the context of 

political limitations of elected and regional persons and bodies. Because the Corps’ 

must complete an environmental impact statement and analysis for their proposed 

lower river project, the opportunity to think outside of the artificial box can be required 

through § 102.2.c of the National Environmental Policy Act. This project document 

seeks to provide some bases for that required analysis. 

We approach this task through the following primary foci: 

1. An analysis of the design flood magnitude and duration that must be 

accommodated by any lower river protective works. 

2. An assessment of potential opportunities for reducing those flood flows through 

enhanced upstream flood storage using natural or small-scale structural 

enhancements that will increase wildlife habitat and amenities for upstream 

landowners and governments in order to encourage their implementation. 

3. Analysis of the unique geologic and hydrologic characteristics of the present 

configuration of the Pájaro Watershed as they control and limit options for flood 

hazard reduction. 

4. Compilation and preparation of a comprehensive database on the watershed in 

digital format that can be shared by the 4 counties and the interested public. 

Additional analyses for the economic feasibility of combinations of upstream and 

downstream flood mitigation efforts, the political economic driving forces that need to 

be acknowledged and accommodated to make a watershed-wide flood control 

solution work, the roles of federal and state agencies in permitting and regulating 

effective solutions, and the environmental constraints and restoration opportunities 

afforded by a watershed-wide flood control project are also woven into the fabric of 

this report. 

Coordination with ongoing work 

Raines, Melton & Carella, Inc. (RMC) have been contracted through the Pájaro 

River Watershed Flood Prevention Authority, formed through coordination of the 

Association of Monterey Bay Area Governments (AMBAG) to consider opportunities 

to increase upstream flood storage through modification of existing reservoirs or 

construction of new flood control dams. Their first report is available through AMBAG 

and, for a limited time, on their website: http://www.rmcengr.com/Pages/prwfpa.htm 

(Phase I). RMC conducted standard hydrologic modeling of effects of urbanization in 

the largely rural upper watershed, and assessed costs of new or rebuilt conventional 

dams that could provide some flood control benefits. The findings basically 

demonstrate that build-out in San Benito County has little net effect on countywide 

and watershed-wide runoff volumes, and that costs for old-style flood control dams 

exceed benefits. One finding of the initial RMC study became the focus of a 

concurrent Phase III study looking at the ephemeral Soap Lake wetland area along 

the upper Pájaro River and lower Llagas and Uvas creeks. RMC concluded that this 

DRAFT 7/22/03 

19 


natural ephemeral basin provided on the order of 30,000 ac-ft of storage and that, 

without it, flood peaks at Chittenden would increase about 137% for the 100-year 

event. The RMC Phase II study, also available now, looks at alternatives in the lower 

valley for bypass and underground floodways and compares them to the various 

Corps’ proposals for levee modification. 

Our work also looked at Soap Lake and considered alternatives for enhancing flood 

storage in a portion of that feature. We did not assume that diminished development 

pressure or conservation-flood easements could preserve all of the existing 

occasionally flooded agricultural land, and thus looked at compensating alternatives to 

allow some levels of development and new highway construction. AMBAG and the 

Watershed Flood Prevention Authority are exploring flood easements for the core 

7900 acres of the site. 

Philip Williams and Associates, Ltd. (PWA) were contracted in June of 2003 by the 

Sierra Club to investigate alternatives not considered by RMC or by the Corps’ as 

publicly revealed to that date. The PWA report, being released simultaneously with 

this report, considers a series of downstream flood mitigation scenarios and links 

some of them to opportunities for enhanced upstream flood detention to reduce 

downstream costs, environmental losses, and maintenance. The PWA studies 

consider stable channel alternatives as well as constricted high-maintenance 

channelization options to provide a wider range of alternatives than have been 

publicly discussed by any entities to date. Among the options considered by PWA is 

one proposed by state and federal regulatory agencies to regrade the channel to a 

“self-maintaining” form. It is designed to transport sediment through the system 

without mechanized assistance, and tries to meet stated goals and objectives of these 

public agencies that must review and approve any chosen alternative. 

U.S. Army, Corps of Engineers (Corps’) is the lead agency for the downstream flood 

control project. The Corps’ has been involved repeatedly following the initial project 

completion immediately after WW II. Their charges include annual monitoring and 

oversight of levee and channel maintenance, repair and resurvey after the 1989 Loma 

Prieta Earthquake and the 1995 and 1998 floods, and design and construction 

oversight of any new flood control project that modifies or replaces their original 

project. City and County governments and citizens have nearly continuously 

requested intervention and design improvements for the Corps’ projects that protect 

the City of Watsonville and the lower Pájaro flood channel. As was revealed in the 

1997 trial of CalTrans for ponding of flood waters associated with the 1995 floods, the 

State of California had always assumed that the Corps’ had responsibility for 100-year 

flood protection for the entire Pájaro Valley and, thus, that highways crossing that 

valley at its lowest point need not accommodate any but local rainfall runoff beneath 

the highway berm. The Corps’ has held repeated public informational meeting and 

tried to use a “stakeholder” process to consider concerns of the lower Pájaro River 

communities. A very considerable effort was initiated in 1998 by the Corps’ to 

critically review past and anticipated future activities of the agency using a nationwide 

in-house professional team (United States Army, Corps of Engineers, 1998), but the public 

has not seem much response from the Corps’ to that foundation report. The agency 

will again attempt to provide a series of alternatives and choose one for final preferred 

evaluation during July 2003. 

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20 













Lani Clough 



Joy Larson 


Steve Mack 


Serena Pring 

Emily Roth 

Amy Thistle 


APPENDICES 

A20

CHAPTER 2 

Design Flood Analysis 

Analysis of Flood Flow Frequency: 

San Benito River, Pájaro River, and Tributaries 

Purpose 

The purpose of this analysis is to determine the discharge of the 100-year 

flow events for several gages on the San Benito River, Pájaro River, Uvas Creek, and 

Pacheco Creek. The 100-year flow frequency events are compared both for all data 

available and at 10-year sub-sets of the flow data. These estimates of discharge were 

calculated using the Log-Pearson Type III methodology as described in Bulletin 17B: 

Guidelines for Determining Flood Flow Frequency by the US Water Resources 

Council (1982). 

Methods 

Data Collection 

Peak annual flow discharge and stage heights at several gages in the 

Pájaro River system watershed. Each gage number, name, river system, and 

drainage area are summarized in Table 1. These data were obtained online from the 

US Geological Survey. 

For the sites at Uvas Creek (11154200) and Pacheco Creek (11193000), 

years with zero flow in the peak record are adjusted to have a discharge of 0.01cfs. 

At the Hollister site (11158500), data for the water year 1957 is missing, and excluded 

from the analysis. 

Data Analysis 

For each gage, the peak annual flow data were ranked by peak discharge 

(Q), with the highest discharge of record with the rank of 1. The data does not have a 

normal distribution, requiring the log of the discharge to be taken for analysis. The 

sample mean (Ŷ LT ), standard deviation (S yLT ), and standardized skew (g s ) are taken 

off the log-transformed discharge (Q LT ). 

Due to the nature of flood events, and the small sample size of extreme 

events, the accuracy of the sample skew is poor. An adjustment is made to the 

sample skew (g s ) for improved accuracy. The adjusted skew used in this analysis is 

adjusted by the following equation: 

g adj = g s * (1+(6/n)) 

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Pajaro Watershed Flood Management

where: 

g adj is the adjusted skew 

g s is the standardized skew 

n is the sample size 

For several exceedence probabilities (p) ranging from 0.99 (1.01-year 

recurrence interval) to 0.01 (100-year recurrence interval), the values of the 

standardized variate K were obtained using tables included in the Bulletin 17B report 

for the adjusted skew value. The Log-Pearson Type III estimates are determined from 

the following equation: 

K 

(g adj ) 

Y LT = Ŷ LT + KS LT 

where: 

Y LT is the log of the estimated discharge for the exceedence probability at 

Y LT is the mean of the log-transformed sample 

K is the Log-Pearson Type III variate determined using the adjusted skew 

S LT is the standard deviation of the log-transformed sample 

The antilog of the Y LT values determined is the estimate of discharge at 

the specific exceedence probabilities or recurrence intervals. In addition, 90% upper 

confidence intervals were set for all stations at each exceedence probability. 

Smaller sub-sets of data from each station were analyzed for flood flow 

frequency at intervals of 10 years. The sub-set analysis of the 100-year flood was 

determined using the same methodology as the Log-Pearson Type III described 

above, including skew adjustment. No confidence intervals were estimated in this 

analysis. 

Results 

The results of the flood frequency analysis for the select gaging stations 

in the San Benito River, Pájaro River and tributaries are summarized in Table 2, and 

confidence intervals are graphed as shown in Figure 1. 

Station Name 

Station 

Number 

Years of 

record 

Calculated 

100-year 

flood Q cfs 

Calculated 50- 

year flood Q cfs 

Calculated 

25-year 

flood Q cfs 

Pájaro at Chittenden 11159000 62 30172.03 26759.25 22654.49 

San Benito at 156 11158600 31 7157.91 7052.91 6813.80 

San Benito near Hollister 11158500 33* 30234.73 21948.87 15034.67 

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22 


Uvas Creek near Gilroy 11154200 35** 7009.29 6994.648 6942.47 

Pacheco Creek near Dunneville 11153000 43** 9187.33 9164.01 9063.46 

Table 2: Summary of flood flow frequency estimates 

* Water year 1957 missing data 

**Adjusted for zero flow years 

50000 

45000 

40000 

35000 

30000 

25000 

20000 

15000 

10000 

5000 

0 

Chittenden upper confidence interval 

upper conf. 

Q estimate 

0.99 0.9 0.7 0.5 0.2 0.1 0.04 0.02 0.01 

exceedence probability 

16000 

14000 

12000 

10000 

8000 

6000 

4000 

2000 

San Benito at 156 upper confidence interval 

upper conf. 

Q estimate 

0 

0.99 0.9 0.7 0.5 0.2 0.1 0.04 0.02 0.01 


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23 


70000 

Hollister upper confidence interval 

upper conf. 

Q estimate 

60000 

50000 

40000 

30000 

20000 

10000 

0 

0.99 0.9 0.7 0.5 0.2 0.1 0.04 0.02 0.01 


8000 

7000 

6000 

5000 

4000 

3000 

2000 

1000 

Uvas Creek upper confidence interval 

upper conf. 

Q estimate 

0 

0.99 0.9 0.7 0.5 0.2 0.1 0.04 0.02 0.01 


20000 

18000 

16000 

14000 

12000 

10000 

8000 

6000 

4000 

2000 

0 

Pacheco Creek upper confidence interval 

upper conf. 

Q estimate 

0.99 0.9 0.7 0.5 0.2 0.1 0.04 0.02 0.01 


Figure 1: Log Pearson Type III results with upper confidence intervals for all gages. 

DRAFT 7/22/03 

24 


The gages at Chittenden (11159000) and at Hollister (11158500) have 

similar 100-year peak floods, and have the highest maximum discharge of the gages 

analyzed. The gage at Chittenden (11159000) has the largest drainage area, but 

does not have the largest 100-year maximum discharge estimate, in part because its 

data set is longer and thus the confidence is better (lower interval). 

The results for the 100-year flow decadal analysis for each gaging station 

are listed in Figure 2. 

140000 

Decadal analysis 

100 year flood discharge cfs 

120000 

100000 

80000 

60000 

40000 

Chittenden 

Gage at 156 

Hollister 

Pacheco C. 

Uvas C. 

20000 

0 

1940 1950 1960 1970 1980 1990 

Figure 2: 100 year flood estimates by decade 

All gages show a small increase in the estimate of the 100-year flood 

discharge from the time period of 1960 to 1990. A decrease is also seen in all gages 

from the 1950 estimate to the 1960 estimate. 

Discussion 

The above analysis was conducted using the standard reference as required of the 

Corps of Engineers. It requires a series of adjustments for extreme value rare events 

to account for their statistical rarity and for the non-symmetrical distribution of 

precipitation and runoff. An oversimplified way of looking at such data sets is that it is 

either raining or it is not raining. If it is not raining, the amount of rain is 0.0 and 

cannot get any less. But if it is raining it can almost always rain harder and get wetter. 

“Dry” is a fixed value but “wet” is not. The adjustments are made using a table to fit 

the data to a certain log-transform that Mr. Pearson called Type III and that fits a great 

many precipitation-related data sets. 

The Corps’ has chosen to design for a 40,100 cfs peak at Murphy’s Crossing, below 

Chittenden. That chosen value is subject to many caveats. The actual calculated 

DRAFT 7/22/03 

25 


value for the maximum possible 100-year flood at Chittenden is closer to 43,500 cfs 

using the Corps’ methodology. But there is flood storage at Murphy’s Crossing, in the 

Aromas area (Aromitas Lake of Jenkins) and in the Soda Lake area just below the 

Chittenden gauge. USGS actually gauges the Pájaro during high flows at the bridge 

at Aromas, not at Chittenden several miles upstream. Earlier chosen design floods 

were higher, but the current value is not unreasonable. Because the lower river is 

formed by spillover from the upper watershed, drainage area does not increase in a 

linear fashion downstream. This is a unique watershed. As we shall show, the 

channel capacity at Soap Lake and in the San Benito River increases in a very nonlinear 

fashion for flows above about 22,000 cfs as gauged at Chittenden. Thus the log 

plot of flows versus return period above that discharge tends to “flatten” (see the X’s 

or actual values in Fig 6 above versus the calculated Log-Pearson III curve). That is, 

high flood flows tend to be smaller than would be predicted based on the full period of 

record because of the shape of the channels in the upper watershed and their faultdammed 

characteristics. The Corps’ design value is thus conservative in that it is 

above reasonably probable values. 

The flow record was disaggregated into separate decades and each was assessed 

individually to look for trends. In practice, one should not use a single gauging station 

to predict a flood magnitude beyond two-times the length of the actual record. That is, 

to estimate a 100-year flood, one needs at least 33 years of peak flow record. Thus, 

the predictions based on 10-year periods do not reflect actual 100-year flow 

predictions, but do give potential clues regarding changes in flood frequency through 

time. From this analysis we see that the 1955 Christmas storm at Chittenden in an 

otherwise non-remarkable decade would have forced prediction of a much larger 100- 

year event, but that the more frequent large events in later decades change that 

predicted value. The Christmas, 1995, flow at Chittenden was estimated at 24,000 cfs 

and was only exceeded there by the February 1998 event at 25,100 cfs. The March 

1995 event was estimated at 21,500 cfs. Thus, the 40,100 cfs figure being used by 

the Corps’ for a design value is 160% of the maximum historic peak in 62 years of 

instrumental record. The February 1938 storms caused the levees to break in the 

lower Pájaro (Monterey Herald, 2-12-38) and flooded the Watsonville area with a 

reported 3 feet of water. A newspaper photo of the lower Pájaro Valley below the 

town of Pájaro (Fig 7) at about the location of Highway 1 today looks very much like 

the 1995 conditions. 

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Figure 7 -- 1938 Lower Pájaro Valley flood. Photo point appears to be near present 

Highway One. 

The lack of gauge record for 100 years at Chittenden does not limit our analyses back 

only to its start in 1940. Study of precipitation records for the periods for which we 

have gauge record permit comparison with those same records for the 40 or more 

years before stream gauge record. Where we have 100-years of record for daily 

rainfall, such as at Hollister, we see that the 1955 event was by far the largest 

cumulative net storm rainfall. Although Hollister recorded 1.0 to 1.38 inches in single 

days in 1935, 1936, and 1937, and although Watsonville and Hollister recorded more 

than 1 inch per day for three consecutive days in 1937, it was the Christmas storm of 

1955 that set the standard for the Pájaro watershed. Beginning December 20 th , Santa 

Cruz mountain summit areas recorded more than 10-inches a day through the 23 rd . 

Hollister recorded 1.93 inches on the 22 nd , 3.75 on the 23 rd , and 1.01 on the 24 th . In 

the southern Santa Clara County area the February 2-4, 1945 storm, with over 10 

inches in a day at Morgan Hill, provided the maximum historical rainfall period, and 

that overlaps with Chittenden discharge record where flow was significantly less than 

in 1955, 1998, and 1995. It is thus reasonable to postulate that the Chittenden gage 

has recorded the largest Pájaro River events of the past 100 years, and that sustained 

high flows must have been greatest in 1955, followed by 1998. 

There is the anomaly of the 1998 flow record at on the San Benito River that merits 

further discussion. The official USGS gauge record indicates that the Pájaro tributary 

peak flow was greater than the downstream flow at Chittenden in 1998. According to 

the U.S. Geological Survey Field Office Supervisor, Larry Freeman, this may reflect a 

real difference where flood storage in the lower San Benito River below the Hollister 

gauging sites retains flow and diminishes the peak at Chittenden. However, the 

gauging station on the San Benito River was washed out in 1998 and the flow had to 

be estimated based on water backed up at the Highway 156 bridge, rendering the 

estimate good only to ± 25 percent (see Appendix 1). Indirect evidence, presented in 

the next chapter on flood storage, supports Freeman’s hypothesis that there is a large 

flood storage volume still available in the Lower San Benito River. 

DRAFT 7/22/03 

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Regional Analysis 

The trend in percent contribution to lower Pájaro flow volumes from the upper Pájaro 

River versus the San Benito tributary deserves some analysis. RMC pointed out the 

apparent shift away from Santa Clara County contributions from the north and 

increased San Benito County contributions from the south. The three major tributaries 

were all dammed for water supply reservoirs about the same time in the 1960’s, and 

all are full during major flood events so there should be no net effect of reservoirs on 

relative runoff from each of the three major Pájaro tributaries. The RMC analysis is 

valuable and included here (RMC, Tech Memo 1-2-1 of October 8, 2001) 

“Basis of Comparison 

The Pájaro River watershed is large and the land uses are varied from dense 

urban to intensive agricultural to grazing lands to unused acreage. Changes in land use 

and management plans can affect watershed behavior. To be sure the hydrologic model 

will address the needs of decision makers and planners, three questions must be 

addressed: what hydrologic parameters are necessary for comparison, where in the 

watershed should these parameters be predicted, and at what exceedence frequencies 

should these parameters be predicted. 

Parameters to be used 

The most widespread parameter used for comparing changes to watersheds is 

“the annual instantaneous maximum peak discharge.” This is the discharge (rate of 

flow) in a stream channel and adjoining overbanks that is the greatest value at any time 

during a water year no matter how long the discharge lasts. A water year is the year 

ending September 30 and beginning the previous October 1. It is assigned the calendar 

year corresponding to the September 30 date. 

The second most prevalent hydrologic parameter is the volume of flow in the 

stream. 

Generally the annual maximum 1-day average discharge value or 3-day average 

discharge is used in highlighting differences in runoff. For the Pájaro River watershed 

the annual maximum 3-day average discharge is recommended because the watersheds 

are generally large and the 1-day average discharge is often reflective of the 

instantaneous peak discharge. 

Two parameters are recommended – instantaneous peak discharge and 3-day 

average discharge. Both parameters are to be annual maximum values. 

Parameters to be predicted 

DRAFT 7/22/03 

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Shown in Table 1 are annual instantaneous maximum peak discharges from 

two longterm stream gages – one on the San Benito River near the City of Hollister 

and one on the Pájaro River at Chittenden just upstream of the end of the Corps of 

Engineers Flood Control project. 

The San Benito River near Hollister gage had a drainage area of 586 square 

miles, while 

the current gage located at Highway 156 has a drainage area of 607 square 

miles. The drainage areas at the two gage locations are within 3.5 percent of one 

another and the combined record can be considered as one continuous record since 

1950. The drainage area at the San Benito stream gage is approximately half of that at 

the Pájaro River at Chittenden gage. Data has been collected on the Pájaro River 

continuously since 1940. The four largest instantaneous peak events shown on the 

following table are in the 1956, 1958, 1995 and 1998 water years. 

The ratios for the peak discharges at the Chittenden gage divided by the peak 

discharges at the San Benito River gage for the four major flood years are: 

Water Year 

Ratio 

1956 3.217 

1958 2.026 

1995 1.287 

1998 0.728 

Because the ratio of the drainage areas at the gages is approximately 2.0, one 

might expect that the peak discharges maintain about that same ratio. However, the 

1956 event, the Christmas 1955 flood, shows much more of the peak discharge 

attributable to the Soap Lake portion of the Chittenden gage’s drainage area. The April 

1958 flood was fairly evenly distributed. The two most recent floods, the March 1995 

flood and the February 1998 flood, had much more of their peak discharge coming 

from the San Benito River portion of the overall watershed at the Chittenden gage site. 

The following table shows the average daily discharges on the two rivers for 

the four largest flood recorded at the Chittenden gage. The ratios of the sum of the 

average flows for the maximum three consecutive days are shown below: 

Date Chittenden San Benito Ratio 

12/1955 45,300 cfs-days 10,040 cfs-days 4.512 




DRAFT 7/22/03 

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Interestingly, the maximum consecutive 3-day flow volume was approximately 

the same for all four major floods on the Pájaro River. The amount of volume 

contributed by the San Benito River watershed, however, has grown from around a 

quarter in the 1950’s floods to around a half in the 1990’s floods. This means that the 

rest of the 1,186 square mile watershed at the Chittenden gage contributed less volume 

in the 1990’s floods than it did in the 1950’s floods.” 

Based on the RMC analysis, above, it would appear that something is changing in the 

Pájaro Watershed system. To investigate further, we looked into storm tracks for the 

1995 and 1998 events based on precipitation and runoff at stations to the west and 

south of the center of the Pájaro Watershed. Appendix 2 includes a map of the 

stations used and plots of precipitation and runoff. 

Storm Patterns: Appendix 2 (Storm Analysis) compares the 1995 and 1998 Pájaro 

Watershed events based on rainfall and runoff stations on both the west and south 

axes of the Pájaro Watershed (see map in that Appendix). The two flood periods 

were associated with fundamentally different storm patterns. The 1995 event was 

shorter and much less intense at Corralitos and Hollister than in 1998, but the 1995 

storm near in the middle San Benito River watershed at Pinnacles National Monument 

was more intense than in 1998. More fundamentally, all stations indicate that the 

1995 peak discharge was nearly synchronous with the rainfall peak; while in 1998 the 

first rainfall peak did not result in a synchronous flood peak, and the 1998 rainfall had 

a longer duration and second period of intensity compared to 1995. What this seems 

to mean is that the 1995 storm stalled right over the centroid of the watershed near 

Hollister and produced an intense 48-hour flood, while the 1998 floods were the result 

of more widespread rainfall for a longer time resulting in flood peaks that were 

possibly near simultaneous, derived from both the upper Pájaro and San Benito 

subbasins. The 1945 and 1955 events were more like 1998 based on their 

widespread rainfall patterns. Standard probability analysis does not, unfortunately, 

differentiate among differing causal mechanisms for standard winter rainfall floods. 

The fact that the 1995 flooding in the Lower Pájaro Valley had a much steeper rising 

hydrograph limb may partly explain why piping (flow under the levees with erosion) 

appears to have contributed to the levee failures in 1995 but not in 1998 even though 

the flood stages below Murphy’s Crossing were similar. These differences are 

reflected in the hydrographs at Chittenden: 

DRAFT 7/22/03 

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DRAFT 7/22/03 

31 













Lani Clough 



Joy Larson 


Steve Mack 


Serena Pring 

Emily Roth 

Amy Thistle 


Draft of July 22, 2003 Public Copy A31

CHAPTER 3 

Upper Basin In-channel Flood Storage and Restoration Opportunities 

Basic Conclusions: 

A very substantial volume of flood storage exists in the upper watershed. Focus to 

date has been on the Soap Lake subbasin of the upper Pájaro and lower Llagas and 

Uvas tributaries. This area is part of the Lake San Benito basin and is very flat with 

poorly integrated drainage. Most of the basin is underlain by hydric soils and is in 

agriculture. The RMC reports have tentatively outlined 30,000 ac-ft of flood storage 

over 7900 acres at an average depth of over 3 feet. That is the area that is subject to 

flooding in the 100-year flood, and approximately corresponds to a portion of the 

FEMA flood delineation map (see Map C for a portion of that map). Our team has 

identified a larger upper Pájaro River area subject to inundation to an average depth 

of 1.5 feet that gives about the same de-facto storage volume (see Map C). Our team 

has identified about 3000 acres of the RMC 7900 acres that could be excavated to 

enhance flood storage for an additional 7700 ac-ft of storage. The excavated material 

could be used for nearby protective berms and fill to allow some non-agricultural land 

uses in the areas subject to very shallow infrequent inundation of 1 foot or less. The 

net result is about 7000 ac-ft of added storage above the passive 30,000 ac-ft that 

already exists. 

On the San Benito River and its tributary Tres Pinos Creek, about the same 30,000 

ac-ft of de-facto passive flood storage exists today, but it is located along in-channel 

and channel margin areas along the braided channel itself. This total 60,000 ac-ft of 

storage capacity modifies the runoff characteristics of the Pájaro River today and all 

flood control designs assume that such storage is functional and in place. Diking of 

sewage lagoons and active in-channel mining operations subtract from that storage 

and increase downstream peak flows. Today’s San Benito River is diked and 

modified so that storm flow volumes and peaks derived from that tributary should be 

increasing. We find that those channel changes have occurred progressively after the 

late 1940’s and 1950’s. We estimate that opportunities exist to enhance flood storage 

on the lower San Benito River below Tres Pinos for an added 14,700 ac-ft without 

encroaching on areas outside of the current (1996) FEMA-defined 100-year active 

flood zone. An example of an area suitable for restoration of natural overbank flood 

storage is shown in Fig. 10. 

Thus the total potential augmentation of flood storage above Chittenden is on the 

order of 22,400 ac-ft. This added volume of in-channel and near-channel storage has 

a direct effect on flood peaks in the lower Pájaro River Valley, lowering the flood 

peaks by about 10,000 cfs and the stage below Murphy’s Crossing by about 4 feet for 

the 100-year design event (see PWA Lower Pájaro report, 2003). We believe that 

there are incentives for costs of upstream flood storage augmentation to be borne by 

local landowners. We believe that a river parkway plan can be combined with such 

augmentation to protect, stabilize, and enhance biotic and cultural resources 

upstream in a win-win situation so that costs of downstream flood protection are 

reduced while biologic and water quality values are increased throughout the 

watershed system. 

DRAFT 7/22/03 

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We also find that on the order of 6000 ac-ft of flood storage on the San Benito River 

south of Hollister was lost before 1955, and that this cannot be recovered today 

because housing and other structures are now located on that portion of the 

floodplain. 

MAP C: Storage areas considered in this report. Inset: 1996 FEMA 100 year flood area 

Theory: 

A balance between a river and its floodplain is necessary for the system to function 

without continual artificial (human) input or damage from floods and/or bank erosion. 

Natural watershed systems are drained by waterways that store sediment and water 

both in the channel and on its floodplain. The floodplain is constructed by the river 

itself as a self-regulating feature for storage of floodwater that exceeds the volumes 

that can be carried in the natural stable channel. Sediment that cannot be carried by 

the system during short flood periods is stored as bars and other deposits in the 

channel and on the floodplain (Curry, 1981) awaiting the next flood flows. 

DRAFT 7/22/03 

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When the balance between the volumes of water and sediment that are supplied to a 

river from its tributaries and from its bed and banks is changed, the river system 

attempts to rebalance itself. Rivers cannot store energy. They must use it as they 

gain it, dropping 300 feet in elevation, for example, from Hollister to the ocean. If 

water flow volumes exceed sediment volumes, the river will attempt to erode sediment 

from its bed and banks to rebalance itself and equilibrate its rate of work with the 

potential and kinetic energy available to it. The river that drains a watershed is 

adjusted to carry the range of floods and sediment inputs that occur naturally in that 

watershed. If a period of major landslide activity occurs, for example along the fault 

zones in the Upper San Benito River, that sediment is stored in the channel awaiting 

sequential years of flood flows to move it downstream. This leads to natural channel 

aggradation, or build-up of sediment in the bed. After this occurs, flood flows 

redistribute that sediment year after year, parceling it out for transport through lowgradient 

reaches downstream. The steep gradients on the depositional areas of the 

San Benito River near Hollister (18-20 ft per mile) are the result of the great natural 

instability of the watershed hillslopes upstream. 

When a river is deprived of sediment or when flood flows exceed the volumes 

necessary to carry the sediment entrained in that flood flow, the river erodes its bed 

and/or banks. Gravel and sand mining in the natural riverbed act to “starve” the river 

of sediment, and lead to channel incision (downcutting) and/or bank cutting. When 

downcutting is severe, the river can no longer store floodwater in its floodplain 

because it cannot access its floodplain as it would naturally do every 2 to 3 years (see 

Fig, 11). If riverbed mining exceeds the long-term natural sediment supply, the 

watershed system is said to be in disequilibrium. That is, the natural form of the 

watercourse and its watershed are no longer balanced with the water and sediment 

that are moving through it. One of the most extreme examples of this imbalance is on 

the Lower Russian River in California where the sediment-starved middle reach 

around Healdsburg has incised as much as 20 feet and is now completely separated 

from its floodplain. As a consequence of this loss of flood storage, flooding 

downstream has increased in frequency and severity to the point that the area around 

the town of Guerneville has become the Nation’s focus for the federal flood insurance 

debacle where people repeatedly claim flood losses that cumulatively far exceed the 

values of the properties (James Witt, personal communication, 1997). At the Monte 

Rio gauge on the lower Russian River, 5 or more “100-year floods” have occurred 

since 1986. 

DRAFT 7/22/03 

34 


Figure11 Cartoon showing how incision reduces flood storage and riparian habitat 

Methods: 

The Pájaro Watershed above the Chittenden gauge was inspected carefully to 

determine where natural floodplain areas were no longer being inundated in major 

floods. The 1998 flood was of a magnitude such that it should have covered most of 

the natural floodplains that function in balance with the Pájaro River and its tributaries. 

If, as the probability plot for Chittenden suggests, the 1998 event was a 30-100 year 

magnitude flood at various places throughout the watershed, then the floodplain 

should have carried water with sufficient depth and velocity to leave a record in the 

surface soils. Surface soil characteristics on a floodplain reflect the depositional, and 

occasionally erosional, passages of flood waters where they are vegetated and cause 

slowing of flood flows. Along the San Benito River, low-lying riverside bench lands 

below the level of the agricultural Lake San Benito land surface have very young 

poorly developed soils that are characteristic of flood deposits formed in the last few 

hundred years (Fig 8). These deposits are very different from the moderately 

developed soils on the higher Lake San Benito and Lake San Juan surfaces (Fig 9). 

The current active stream channels do not have any silt-size organic-rich soil 

development at all. Thus, it is possible to differentiate unambiguously where 

floodplains have been abandoned in the last century. 

Surveying of channel cross-sections and elevations was done at several places to 

compare with historic data. A good plane table topographic map was made in 1917- 

1919 in the Hollister area (Hollister, USGS, 30-minute quadrangle) and 

DRAFT 7/22/03 

35 


photogrammetric maps were made based on aerial photography taken between 1952 

(San Juan Quad) and 1955 (Hollister Quad.) Tres Pinos Quad photos were made in 

1953. The date of the published map is not material to the reference elevations, nor 

are the dates of photorevisions. The topography is based on the original aerial data 

except where specifically noted in purple overprint. For all of the upper Pájaro USGS 

quadrangles, published revisions in the 1970’s, 1980’s and 1990’s all specifically note 

no topographic revisions after the original 7.5 minute quadrangle aerial base surveys. 

Field surveys in 2003 augmented a very detailed photogrammetric and 2-foot contourinterval 

ground-based survey made privately for the San Benito River area by 

Graniterock Company. Those December 2000 data with very detailed aerial 

photography at a scale of 1-inch = 500 feet were provided to us digitally by 

Graniterock. The earliest topographic surveys of 1917-1919, as published in the 1921 

USGS topographic map, were made on site by plane table and alidade. Although the 

contour interval on those maps was only 50 feet, the surveyors clearly and definitively 

noted the heights of the stream banks with a “step” in the contour at the break in 

slope. By measuring the stream gradient on the map and the length of the step at 

map scale, the heights of the banks can be estimated. For the upper San Benito 

River above Hollister, those banks were 7 to 8 feet high at the time of the early 

surveys. 

San Benito County staff cooperated to provide access to their mining operation files, 

and to the plat maps and property records so that we could tabulate and attempt to 

contact all property owners bordering the San Benito River below Tres Pinos. These 

records are tabulated in Appendix 3. Those property owners were contacted where 

possible and state, federal, and local agencies were polled to try to learn of their 

concerns and interests in upper Pájaro watershed watercourses (Appendix 4). Field 

investigations were conducted on the Llagas, Uvas, and San Benito tributaries as well 

as portions of the main stems of the Pájaro. We investigated evidences of active 

channel modifications, gauging station status, riverbed and bank conditions, 

evidences of bed-form and plan-form erosion or change, and high-flow markers or 

field evidence. These observational data are integrated into our findings and 

opinions. 

Findings: 

Channel Incision: 

We verified earlier reports (Goldner Associates, 1997, ) that the San Benito River had 

been incising. Our findings for the thalweg elevations along the uppermost San 

Benito above Hollister are as shown in this table: 

DATE 

Blossom 

Rd 

Hospital Rd Union Road Nash Road 

1917-1919 350 ft elev 320-25 ft.elev 298-99 ft.elev ~275 ft elev 

1955 330 ft elev ~308 ft elev ~295 ft elev 269 ft. elev 

2000-2002 314.4 ft. elev 280.7 ft. elev 259.1 ft. elev 

DRAFT 7/22/03 

36 


Although Hospital Road shows some aggradation after 1955, all of the other data 

indicate progressive incision. The Hospital Road data may reflect the annual filling 

that takes place there for a summer road across the streambed. In this Hollister 

section of the San Benito River, the natural floodplains had been abandoned by 1955 

and development was taking place on them. In 1995 and, especially, in 1998, the 

flood flows that were confined to an incised channel, cut laterally and made the 

channel as much as 3 times as wide as before those floods. This is the natural way 

that a watershed system works to regain equilibrium. Lacking overbank low-velocity 

water storage, the deep high velocity flow undermines and cuts the easily eroded 

sand and gravel banks. This provides the sediment load that the high velocity 

confined river is capable of moving, and it begins the process of cutting a new flood 

plane at the lower level of the streambed. This lateral erosion will continue until the 

width of the new deeper channel is sufficient to expend the available energy of the 

flowing water against the stream bed itself with little energy left for bank cutting. In the 

case of the San Benito between Hospital Road and Hollister, this will be about a 0.75- 

mile width if no reclamation is undertaken. As this occurs, the constructed features 

and bridges will be damaged or lost, as is seen in the case of this newly-built Cienega 

Road house during the 1998 floods (Fig 12): 

Figure 12 - House along Cienega Road south Hollister, 1998 

The detailed Graniterock aerial photos permitted us to investigate the entire 

channel below Hospital Road to the junction with the Pájaro. We were 

unable to receive landowner permissions to survey most of that channel and 

needed to investigate the majority of the channel where public bridge rightsof-way 

do not exist, and thus where the channel is not constricted artificially. 

The Graniterock aerial photos and the accompanying 2-foot contour interval 

maps are only a year old and reflect today’s conditions. These permitted us 

to compare the present topography of the river with that in the 1950’s as 

mapped by the US Geological Survey, and with sequential aerial 

photographs. We borrowed and digitized the Soil Conservation Service 

historical aerial photo enlargements of August 1959, and copied the available 

collections from the University of California Map Library and elsewhere. 

These included the 1931 lower Pájaro Valley, 1939 entire river, 1952 and 

DRAFT 7/22/03 

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1967 flight lines and the full digital 1998 federal digital orthophoto quadrangle 

series. 

We learned that there were three classes of change in the San Benito River 

channel that all affect downstream flood peak heights. There were two 

different kinds of land use changes that affect runoff timing and volume to the 

upper Pájaro channel derived from San Benito and Santa Clara counties. The 

changes we document can be summarized in 5 classes as follows: 

1. Those where direct channel incision prevents or reduces overbank 

flood storage onto a floodplain along the river. Rather than model the 

degree of incision necessary to affect flood storage on floodplains, we 

simply noted abandoned floodplains recognized by soils and 

vegetation. This kind of change greatly accelerates passage of 

floodwaters downstream, except where the channel incision intercepts 

the groundwater surface and vegetation thus chokes the channel to 

slow water velocity. 

2. Those where channel widening with or without a deeper central 

channel (thalweg) effectively increase the capacity of a channel and 

thus reduce the height of a flood and access of those waters to their 

floodplain. This kind of change accelerates flood runoff because the 

water remains in the channel and flows at a higher velocity than would 

overbank floodplain flow. 

3. Those associated with a change from a multi-thread or braided 

channel to a single more efficient channel, often accompanied by 

reduced in-channel vegetation. This kind of change accompanies 

incision and is favored where a central channel is deliberately graded 

or confined to protect banks from erosion or to prevent lateral 

migration of the channel, as for example where sewage lagoons or 

highways are being protected. This kind of channelization change 

greatly accelerates flow and reduces flood storage. 

4. Those associated with a straightening and cleaning of seasonal or 

flood-period temporary drainage channels on the floodplain. This was 

observed today only in the Soap Lake area but these same 

constructed drainage channels also are seen in 1917 mapped on the 

now-abandoned floodplain south of Hollister. This class of changes 

reduces the time that overbank floodwater remains out of the channel, 

thus having a modest impact on downstream flood height. 

5. Those associated with dams and flood control structures and bank 

protection measures that harden banks, reduce bank and bed 

roughness, and reduce infiltration capacity and land surface runoff 

detention during intense rainfall events. Public works projects such as 

bridges, spillways, and highway berms tend to reduce bank and bed 

friction and thus accelerate runoff. The farther upstream or farther 

from the channel that these works are found, the less the degree of 

direct impact on peak flood heights. No matter how intense the rainfall 

or how long its duration. Uvas, Chesbro, and Hernandez reservoirs 

DRAFT 7/22/03 

38 


clearly attenuate (reduce) flood peaks for events when they are not 

full and spilling. The RMC report concludes that: 

“The three large reservoirs in the watershed – Hernandez, Uvas and 

Chesbro – have been very effective in reducing the peak discharges of 

the more frequent events and, in the case of Hernandez Reservoir, have 

been effective in reducing peak discharges across the frequency 

spectrum.” (RMC Hydro Technical Memorandum, 2000). 

That report concluded that, in 1937 before the three major water 

supply reservoirs were constructed, the 100-year discharge at 

Chittenden would have been about 12 percent larger than today. 

We disagree. That modeled value is based on observed historical 

attenuation of flood peaks below those reservoirs. We investigated 

the watersheds above two of those reservoirs and did not find 

evidence of hillslope overland flow in the oak woodlands that 

represent the conditions that existed in the reservoir basins before 

they were constructed. We thus disagree that the 100-year peak 

intensity rainfall and runoff event would be detained or attenuated by 

a full and spilling reservoir system. The opposite should be the case 

because a full reservoir with super-elevation at the spillways will not 

absorb or detain any more rainfall and thus peak discharges at the 

extreme event are increased unless these water supply reservoirs are 

first drawn down. Flotsam around the shorelines of Uvas and 

Chesbro show that they both have filled to above the elevations of the 

spillway inverts. 

Dikes along both Llagas and Uvas creeks in Santa Clara County and 

significant channelization and straightening of the primary channels 

had led to loss of fish passage and high velocity channel erosion in 

some places. Much of this is now being repaired and channel 

roughness elements are being put in place to try to rebalance these 

tributaries. Our impressions were that the channels themselves are 

now as rough or rougher than were their natural antecedents, 

particularly where filled with Arundo and other plants, and tortuously 

threaded through urban areas. Thus, acceleration of runoff is minimal 

(Fig 13 photos are examples of Llagas conditions) 

DRAFT 7/22/03 

39 


Fig. 13 Two views of the Llagas Creek Channel showing roughness 

elements. Left image is just above Soap Lake, right in central urban 

area 

Channel Diversion 

For the Lower San Benito River, the Graniterock aerial photos and contour 

maps permitted us to establish that a local mining strategy has been to 

isolate various portions of the channels and to protect mining areas and 

channel banks with berms. Some of these berms are built to the same height 

as the natural Lake San Benito lakebed land surface. That elevation assures 

that the berms are above any historic level of the river. The berms and dikes 

reduce access by floodwaters to the full channel width and the incision 

reduces access to adjacent floodplains so that the river is greatly constrained 

and downstream flooding is increased. Figs 18-21 (Appendix 5 – Historical 

Change in the San Benito River) show an example of this kind of 

manipulation in the lowermost reaches of the San Benito River just upstream 

from San Juan Road. Fig 18 is from the December 2000 Graniterock survey 

and shows Highway 101 at its junction with Highway 129, and San Juan 

Highway. The “A”s are placed on abandoned floodplain remnants. A road is 

seen going from the sand mining operation area upstream (right) along the 

crest of a constructed berm that is the same height at the Lake San Benito 

agricultural lands. This berm thus isolates the present river from its floodplain 

remnants, some of which are used for mining equipment storage and some 

for agriculture as was the case in the earlier photographs (Fig 19, taken in 

1939). Topographic detail can be seen in Appendix 6. Modifications from 

1950’s through the 70’s are shown on the 7.5 minute USGS Quadrangles 

shown in Fig. 20 

Channel diversions are found throughout the Pájaro River basin north of Tres 

Pinos. Because the natural channels in both Santa Clara and San Benito 

counties were braided or wide and changing from year to year, early property 

owners confined the channels widely. Llagas Creek is now confined by 

berms over much of its length. Uvas is confined by major levees through 

Gilroy. San Benito River is confined to protect the City of Hollister, to protect 

various sewage treatment facilities, and to protect agricultural uses. 

Agriculture and development do not exist on most of the natural floodplain 

except above the City of Hollister where most of the floodplain is developed 

and where gravel mining and public works has resulted in many training and 

confining dikes. Below (downstream) of Hollister the natural floodplain is 

used for cattle grazing and for a single sod farm. The Pacific Sod Farm 

(Tom Galdos, personal communication, 2003) has cooperated to protect its 

primary growing area with a low berm that was overtopped in 1998. 

Overbank silts are needed for the operation of this farm, where each sod crop 

excavates a portion of the soil resource, and we were told that production is 

becoming marginal without further sediment accumulation. 

RESTORATION OF CHANNEL FUNCTIONS 

We estimate that an average one-fourth mile width of the 6.5-mile long lower 

San Benito River below Highway 156 could be restored to provide an 

DRAFT 7/22/03 

40 


average 8-foot depth of water that is not now being stored at flood stages 

above that of a 25-30 year recurrence interval. To reclaim this storage 

volume mid-channel levees would have to be breached, incised channels 

would have to be recontoured or confined by gabion baskets or other 

structures or plantings to slow peak flood flow volumes, and overwide 

channel reaches would need gabion structures or plantings to constrict flow 

to a central meandering channel. 

Non-structural solutions, primarily involving willow plantings, have been 

effective in the Carmel River for this kind of restoration of a low-flow central 

channel that supports wildlife and protects riverbanks from erosion. The San 

Benito River is more problematic than the Carmel. Unlike the Carmel, 

aggregate mining is a primary tax base for San Benito County. Further the 

channel of the San Benito (but not Upper Pájaro) has a very low base flow 

and is dry much of many years, thus making vegetation management more 

difficult. The history of mining and degree of channel incision that has 

resulted on the San Benito create a more immediate need for active solutions 

that will set the stage for raised water tables, increased in-stream vegetation, 

and slow aggradation of the active riverbed. 

Suggested Restoration options for San Benito River: 

Two primary restoration strategies must be used on the San Benito River. 

The levees and dikes that exist within the channel must be breached at 

sufficient points to allow ready and rapid exchange of floodwaters throughout 

the channel. This will create a floodway, or zone of active flood storage. It is 

important that this storage be “on-channel”; that is, readily able to retain 

floodwater as the stage rises in the river. All of the berms need not be 

removed, but the more that can be removed, the greater the storage capacity 

of that active channel. For sites like the Hollister sewage lagoons, the levees 

cannot be breached, but for sites such as shown in Appendix 5, they must be 

breached. For a site like the Pacific Sod farm, where an entire meander is 

protected by a berm, some accommodation can be made to allow flooding 

only at flood stages of 25-year return period or greater. This is about the 

magnitude where these protective berms overtop today. 

For the overwide channels and other sites where floodplains have been 

abandoned directly along the San Benito River channel, we recommend 

consideration of a series of gravel-filled gabion baskets that extend from the 

banks toward an optimal central channel. These structures do not cross the 

channel and do not impact the low-flow channel. The serve as a series of 

confining and “training” structures that focus the flow of the river in a singlethread 

central channel, while simultaneously creating flow velocity reduction 

against the banks and sediment deposition zones. As the central channel 

becomes defined after one or more channel-forming events (see Rosgen 

figure on p 16), then a second and third set of baskets are built on top of the 

first until the grade of the channel at flood stage is high enough to reach the 

floodplain and restore stable channel geometry. If properly placed, the 

gabion basket assemblages will encourage pool and riffle geometry in the 

central channel, and will allow vegetation to become established along the 

base of the present riverbanks. That vegetation is the primary tool for 

reducing bank erosion and for slowing the flood velocities. In effect, each 

DRAFT 7/22/03 

41 


“lift” or set of gabion baskets becomes a control structure for a new floodplain 

in the overwide channel areas, 

If sediment supply were very large and aggregate mining were not occurring, 

it would be a simple matter to allow the channel to aggrade to sequential 

gabion installations until the system was returned to a condition similar to that 

prior to human alteration. But sediment supply is episodic and not unlimited 

as is demonstrated by the ever-widening channels (see Riley, 2003). 

Further, the aggregate industry owns much of the channel and its banks and 

is the logical entity with the capability to stabilize and restore the river 

channels. 

Aggregate Mining Company Opportunities: 

We tabulated and plotted all riverside ownerships (see Appendix 3). The 

Granite Rock Company of Watsonville, California, owns or controls the major 

portion of the channel between the Pájaro confluence and Tres Pinos. They 

lease surface portions of their parcels for farming on the Lake San Benito 

soils, and extract aggregate resources from the channel bed, usually by 

“skimming” the active braided bed. Their active mining operations ceased in 

this area 5 years ago. There are other aggregate operators on the river, and 

all are in theory regulated by both the State and the County (see Appendix 7). 

Regulation is not consistent or effective. The State, under the Surface Mining 

and Reclamation Act (SMARA) requires a Reclamation Plan and financial 

assurances (bonding) for each operator. This program is administered by 

San Benito County. The State has no authority over land use permits, so the 

County is also responsible for either issuing a Conditional Use Permit or 

making specific findings that may allow “grandfathered” projects as vested 

uses. Thus, San Benito County carries the primary responsibility for 

oversight of an industry that provides an important part of its tax base. 

According to the California Department of Fish and Game (personal 

communication, Santa Rosa office, 2003), some San Benito River operators 

may not be in compliance with their Section 404 regulations for in-channel 

modifications. According to some operators, San Benito County is attempting 

to limit their operations, in part because of complaints by riverside 

landowners about bank erosion (such complaints were heard from many 

property owners that we contacted). This environment restrains mining 

operations, with some operations currently shut down awaiting permits. We 

see an opportunity to use aggregate mining operators, with access to heavy 

equipment and aggregate resources, to help provide a solution. 

A San Benito River Parkway Plan needs to be developed to stabilize and 

restore the lower San Benito River. At the present time, public respect for the 

river is very low. Both access and amenities are rare. Many residents of that 

county only see the river from highway bridges and have no idea what is 

actually in the channel. Where the channel has incised to the water table and 

mid-channel willow thickets exist, local residents and the County complain, 

with some validity, that flood flows are then forced into the banks with 

resulting erosion. Where roads access the channel or banks, refuse is 

dumped to be carried away by subsequent floods. Temporary summer river 

crossings, as at Nash Road and Hospital Road, are installed seasonally with 

DRAFT 7/22/03 

42 


culverts and fill. Other parts of the channel are used for off-road vehicle 

recreation resulting in destruction of the veneers of gravel cobble bed armor 

leading to erosion with only minimal flow velocities in subsequent winters. 

Exotic vegetation in the channel provides a seed source that spreads to 

adjacent agricultural fields. 

Graniterock has shown us its willingness to discuss and promote restoration 

options, including a River Parkway. They are on record with such a proposal, 

and conducted the channel survey for just such a purpose. For them, the 

incentive is continuing County cooperation and permitting through all 

regulatory agencies. They want to access the aggregate resources. For the 

riverside landowners and the County Public Works agency, the incentive is 

reduced erosion and maintenance costs. For the local residents, the 

incentive is a potential river parkway with 10 or more miles of high-value 

riparian parkway and habitat, and some public access. For the downstream 

counties, the incentive is flood storage and reduced loss of lands and costs 

downstream for flood control. This is a potential win-win situation. 

Practically, such restoration planning and implementation takes time. Some 

areas must be maintained for mining if the operators are to cooperate and 

provide support for the restoration. Because of the high value of the 

agricultural production on the Lake San Benito silt soils, mining aggregate offchannel 

is not practiced locally. Because mining does not take place during 

flood periods or when groundwater levels are high, operators need to mine 

and stockpile in the dry season. A well-designed restoration plan that 

attempts to integrate aggregate resource mining is not a tautology. It can be 

done. The Merced River parkway, the San Joaquin River Parkway, and 

several other California examples provide models. Enhanced flood storage 

accrues slowly. It may take decades to achieve the full component of 

potential enhanced flood storage. You cannot simultaneously aggrade and 

mine the same parts of the channel. Mining must be focused on those sites 

where there are minimal streamside potential flood storage areas that can be 

restored. Gabion baskets would have to be installed in areas not being 

mined as well as in areas being mined. As many as three tiers of baskets 

may need to be placed initially just to bring high flood flows up to floodplain 

grade, but mining can continue between those tiers of baskets. We are 

working to restore what is called the energy grade line of the surface of the 

flood flows at 25-30-year magnitude events only. We can allow all other 

lesser floods to pass down a central thalweg. Fig 14 is a cartoon that 

illustrates this open central channel. Unfortunately, the USDA Stream 

Restoration Best Management Practices web site does not provide examples 

of these 1-km wide scale restoration structures, but the principles that they 

illustrate are often applicable 

(http://www.wcc.nrcs.usda.gov/watershed/UrbanBMPs/stream.html). What is 

important is the fact that the structures are low-tech, porous, inexpensive and 

do not obstruct the central channel. Like the Stream Barb structure used in 

smaller channels (Fig 15), the gabion basket structures slow water at the 

edges of the channel and are easy to install and maintain. 

We recommend that Graniterock and other willing San Benito River 

aggregate mining operators be invited to develop plans for a restoration/river 

DRAFT 7/22/03 

43 


parkway system that can be implemented with no or minimal outside funding. 

Graniterock has already demonstrated a willingness to propose such action 

and assisted our study through their generous sharing of their aerial survey 

data. If conservation easements or land trust arrangements can be 

implemented for parts of the upper Pájaro watershed in conjunction with 

these major landholders, this may facilitate faster completion of potential 

storage volumes. We can help to facilitate such planning and 

implementation. 

Suggested Enhancement Options for Upper Pájaro River: 

The Upper Pájaro River, along the Santa Clara-San Benito County line is 

fundamentally different than the San Benito River. Here a channel is incised 

up to 25 feet below the Lake San Benito lakebed, but because the riverbed 

has historically carried a reliable supply of influent groundwater, a dense 

finger of riparian forest characterizes most of the channel. This mature 

riparian forest of cottonwood, alder, maple, and willow has a dense woody 

instream fabric of logs and mid-channel growth, with a diverse pool structure. 

Although only 100 m wide in places, this riparian corridor provides high 

quality wildlife habitat and, apparently, allows anadromous fish passage into 

Llagas and Uvas creeks. 

Because the riparian forest is so dense and woody debris so prevalent, flood 

stages rise rapidly and go overbank onto the old San Benito lakebed. Local 

landowners report that flooding reaches the old lakebed level at a frequency 

of 10 years or less. Because of the high regional groundwater levels that 

seasonally saturate up to the lakebed silt cap, the soils of the area are 

classed as hydric and, unless cropped continually, revert to wetland 

conditions with emergent wetland plants. Farmers have constructed drainage 

channels across these lands to carry shallow groundwater and rainfall into 

the Pájaro. 

We were able to meet with local landowners and/or farm leaseholders. We 

learned that this Soap Lake area, just south of Gilroy, and situated along 

Highway 25 between Gilroy and Hollister, may be a target for extensive 

development. An ongoing effort sponsored through the Pájaro River 

Watershed Flood Prevention Authority and AMBAG seeks to establish flood 

or conservation easements for the Soap Lake basin. Our sources suggest 

that the opportunity costs for development are so great that contiguous 

easements may be very difficult to obtain. While the site looks like marginal 

agricultural land used for little more than growing hay or grazing with small 

areas of row crops, it is in fact being leased back to local farmers and kept in 

agriculture as an interim holding pattern while development options are 

considered. If some of these lands would be wetlands were it not for 

continual agricultural use, then federal regulations will make it necessary to 

maintain agricultural uses or raise the lands or protect them with dikes and 

levees to permit non-agricultural uses. Should this be the case, a need for 

local fill may provide an opportunity to encourage landowners to excavate the 

3-foot deep lake-silt cap immediately adjacent to the river. This could 

increase the flood storage. 

DRAFT 7/22/03 

44 


Our modeling of enhanced flood storage considers opportunities for local 

landowners to enhance wetland status in areas now in agriculture through 

excavation of 2 to 3 feet of native surface lake silt (see Map C). There is no 

assurance that the expensive regarding efforts would be cost-effective for 

owners wishing to develop parts of the margins of Soap Lake for housing or 

other non-agricultural uses. Preliminary discussions with representatives of 

landowners have not discouraged us from considering three-foot excavation 

in about 2.5 square miles of lower Soap Lake along the Pájaro River for onchannel 

flood storage augmentation, yielding 4800 ac-ft of new storage in 

addition to the existing Soap Lake flood volume. We have also modeled an 

added 2.25 square mile area extending westward to the existing railroad bed 

berm, adding an additional 2880 ac-ft of new storage, and raising the land 

elevation between Highway 101 and the rail line above flood levels. This kind 

of tradeoff must be approved by all regulatory agencies. In essence, a 

marginal non-functional wetland area now in agriculture is converted to 

functional restored planted natural wetland in exchange for allowing fill of the 

edges of the Soap Lake basin that are only wet during sustained 100-year 

flood events at the present time. Of the 30,000 ac-ft Soap Lake basin 

storage volume, some 700 ac-ft of natural storage would be traded for about 

7000 ac-ft of enhanced functional wetland habitat storage. This is also a winwin 

situation if a developer or regional agency can be found to champion that 

large-scale set-aside, and if the regulatory agencies favor it. 

CONCLUSIONS 

Over 60,000 ac-ft of flood storage exists on or very near the channels of the 

upper Pájaro watershed. Soap Lake comprises an important part of this, but 

only a part of the storage that can be modified or lost with upstream 

development. Approximately 22,400 ac-ft of storage enhancement is readily 

possible. Most of this storage is no longer active and no longer accessible to 

the river because of stream channel incision, levees and berms, and 

diversions. Restoration of this volume can reduce downstream peak flood 

heights by on the order of 4 feet during a 100-year flood. The cost of this 

flood reduction is believed to be less than the cost of protective works 

downstream that achieve the same level of protection. 

DRAFT 7/22/03 

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Lani Clough 



Joy Larson 


Steve Mack 


Serena Pring 

Emily Roth 

Amy Thistle 

Melanie Vincent

APPENDICES & Figures 

APPENDIX 1: Note on 1998 records for upper river flows 

Message 

From: 

Subject: 

To: 

Cc: 

Monday, May 13, 2002 9:44:13 PM 

lfreeman@usgs.gov 

Re: San Benito vs Pajaro 1998 peak question 

Bob Curry 

lfreeman@usgs.gov 

Bob. I had thought your inquiry about 1998 peaks for San Benito 

at HWY 156 and Pajaro R at Chittenden had been responded to several 

months ago. Apparently not, so here is some feed back. 

The Feb. 3 Tres Pinos peak was determined using a slope area and 

an outside high water mark at a location near where the washed out gage 

was last seen (best guess). The peak totally changed the channel. The 

slope area discharge was calculated to be 27,200 cfs, rated Poor with a 

comment that the calculation is "No better than +/- 25% uncertainty". 

This yields potential peaks of 20,400 to 34,000 cfs. 

The Feb. 3 peak value for San Benito at HWY 156 was also a result 

of a slope area using the gage height from the Crest Stage Gage (the 

digital record was faulty because of a huge debris jam at the orifice 

location). Again, the peak totally changed the channel. The slope area 

discharge was calculated to be 34,500 cfs and rated Poor with a comment 

that it is " no better than +/- of 25% of true". This yields peaks that 

could range from 25,875 to 43,125 cfs. There was also a float 

measurement made just after the peak and two follow-up recessional 

measurements made that were used to define the new rating. At the end 

of the 1998 WY, we lowered the datum 3.0 feet in order to avoid gage 

heights of less than zero, caused by the channel scour. The published 

GH for the 2/3/98 peak did not incorporate the datum change as it had 

not yet been made. Peaks for the 1999 WY and later do incorporate the 

additional 3 feet. 

The Feb. 3 Pajaro River peak of 25,100 is during a period of 

record that is rated poor (at least +/-8% potential for error) and is 

based on actual GH record adjusted to surveyed outside high water marks 

of excellent quality. Recessional measurements were made on Feb. 4 

(29.23 GH/17,700 cfs) and Feb. 15 (6,040 cfs). Both were used to define 

a new rating, so the comment in the annual report about rating 

extension being based on slope conveyance is not correct. It's my fault 

for leaving it in the manuscript. I have no record of when the slope 

conveyance was run and subsequently used. The upper end of the new 

rating (40) was based on the two measurements made on the recession 

from the peak. 40 merges with upper end of R 38 and extends only 1.30 

feet higher than 38. Rating 38 was put into effect on the March 1995 

flood peak. The rating extension was only 7,400 cfs above the highest 

DRAFT 7/22/03 

46 


measurement and only 2,100 cfs higher than rating 38. It is still a 

peak of record as are the peaks for San Benito and Tres Pinos. 

Please note that there is a major tributary entering the Pajaro 

River upstream of the confluence of the Pajaro and San Benito rivers. 

Uvas Creek has a drainage area of 71.2 square miles at the old USGS 

gage (1959-1992) Uvas Creek near Gilroy (11154200). I don't know what 

the DA is at the confluence with Pajaro. We don't know what the flow 

contribution or timing of the peak for Uvas Creek actually is. Peaks 

are regulated by Uvas Reservoir. Santa Clara Valley Water District now 

operates this gage. I would like to take over the operation of that 

gage once again as the peak flows seem to be a key element for 

validating flows at Chittenden. 

Another item to note is that the peak at Chittenden occurred 45 

minutes before the peak at the San Benito site. If one looks at the 

total runoff in acre feet for both of the sites, the numbers make 

sense. The total runoff at Chittenden was much higher. February ACFT 

for San Benito at HWY 156 was 130,500 while ACFT for Pajaro at 

Chittenden was 387,500. 

Other factors which are being overlooked or unknown are; 

1) there is a huge, natural, heavily forested and overgrown 

floodplain area where the San Benito meets the Pajaro that acts as a 

reservoir to store peak flows. I don't know how much it could put into 

storage and then release. It's not too hard for me to imagine this 

possibility looking at the height of the post-flood drift in trees I 

could see from HWY 101. 

2)there is also a large area of low lying farmland on the San 

Benito R above this area which was under several inches to feet of 

water. This storage component is very real. If one compares the 

hydrographs for San Benito vs Pajaro, the San Benito peak is much more 

flashy than the Pajaro peak. This is a common occurrence for flood 

peaks at these two sites. 

Given all of the above, including the large uncertainties in the 

Slope Area measurements, I see no big problem here. 

I have also made a suggestion to the US Army Corp of Engineers to 

develop a plan to map flooded areas and run calculations for storage 

the next time we see a major event. They too were concerned with the 

apparent numerical discrepancies between peak discharges at these two 

sites. My contact at the San Francisco office is Carlos Hernandez. 

Larry. 

Larry Freeman 

Field Office Chief 

USGS 

3239 IMJIN ROAD 

DRAFT 7/22/03 

47 


APPENDIX 5 Example of Historical Changes in the Lower San Benito River 

Fig 18-19: Top photo, December 2000; bottom photo, June 1939 

See Fig 20-21for topographic maps of this site. River flow is from right to left. Overbank 

floodplain areas are clearly visible in 1939, as is a wide aggrading sand-filled channel. Mining beginning 

in the 1940’s has now lowered the channel 15-20 feet or more to intersect groundwater. An incised 

channel can be seen in the vegetated mined-out area today. Some areas of original flood plain in 1939 

DRAFT 7/22/03 

48 


are now occupied by industrial development along Highway 101 and along San Juan Highway north of 

Anzar High School. 

Historical Change in San Benito River Just above Hwy 101 

Fig 20. Portions of San Juan Bautista and Chittenden 1:24,000 topographic quadrangles 

showing 1952 topography with mining that was interpreted as active in 1997-98. The purple overprint 

convention differs between the two matched maps, but streambed alteration is indicated over most of 

the original channel area. 

Fig 21 Topography based on the December 2000 photobase. Levees isolate active channel 

from both historic and newly excavated floodway. See text for details. 

DRAFT 7/22/03 

49 


APPENDIX 2: 1995 and 1998 Storm Comparisons (see text for discussion) 

DRAFT 7/22/03 

50 


25 

Pinnacles National Monument Precipitation & Willow Creek School Hydrograph for 

1995 

6000 

20 

5000 

15 

precip (cm) 

10 

4000 

3000 

2000 

Q (cfs) 

5 

1000 

0 

0 

31/Mar 

30/Mar 

29/Mar 

28/Mar 

27/Mar 

26/Mar 

25/Mar 

24/Mar 

23/Mar 

22/Mar 

21/Mar 

20/Mar 

19/Mar 

18/Mar 

17/Mar 

16/Mar 

15/Mar 

14/Mar 

13/Mar 

12/Mar 

11/Mar 

10/Mar 

9/Mar 

8/Mar 

7/Mar 

6/Mar 

5/Mar 

4/Mar 

3/Mar 

2/Mar 

1/Mar 

Pinnacles National Monument PRECIP (cm) cumulative precip (cm) San Benito River near Willow Creek School Q (cfs) 

16 

Pinnacles National Monument Precipitation & Willow Creek School Hydrograph for 

1998 

3000 

14 

2500 

12 

precip (cm) 

10 

8 

6 

2000 

Q (cfs) 

1500 

1000 

4 

2 

500 

0 

0 

28/Feb 

27/Feb 

26/Feb 

25/Feb 

24/Feb 

23/Feb 

22/Feb 

21/Feb 

20/Feb 

19/Feb 

18/Feb 

17/Feb 

16/Feb 

15/Feb 

14/Feb 

13/Feb 

12/Feb 

11/Feb 

10/Feb 

9/Feb 

8/Feb 

7/Feb 

6/Feb 

5/Feb 

4/Feb 

3/Feb 

2/Feb 

1/Feb 

Pinnacles National Monument PRECIP (cm) San Benito River near Willow Creek School Q (cfs) cumulative precip (cm) 

Precipitation data from the National Park Service for Pinnacles National Monument at 

the station of the east entrance (point 004 on map), available at: 

APPENDICES 

A52

http://12.45.109.6/pls/portal30/get_input.make_parmsl_bdate=03-01-1995&l_edate=03-31- 

1995&site=17&par_abbr=RNF&format_out=ASCII, accessed 27 May 2003. 

Stream Discharge data from the U.S. Geological Survey for the San Benito River near 

Willow Creek School (point 005 on map), available at: 

http://waterdata.usgs.gov/nwis/dischargesite_no=11156500&agency_cd=USGS&format=rdb&b 

egin_date=02/01/1995&end_date=04/30/1995&period, accessed 27 May 2003. 

16 

14 

Hollister Precipitation & San Benito Hydrograph for 1995 

9000 

8000 

12 

7000 

precip (cm) 

10 

8 

6 

6000 

5000 

4000 

3000 

Q (cfs) 

4 

2000 

2 

1000 

0 

0 

31/Mar 

30/Mar 

29/Mar 

28/Mar 

27/Mar 

26/Mar 

25/Mar 

24/Mar 

23/Mar 

22/Mar 

21/Mar 

20/Mar 

19/Mar 

18/Mar 

17/Mar 

16/Mar 

15/Mar 

14/Mar 

13/Mar 

12/Mar 

11/Mar 

10/Mar 

9/Mar 

8/Mar 

7/Mar 

6/Mar 

5/Mar 

4/Mar 

3/Mar 

2/Mar 

1/Mar 

San Benito Precip (cm) cumulative precip (cm) San Benito River at HWY 156 near Hollister Q (cfs) 

25 

Hollister Precipitation & San Benito Hydrograph for 1998 

25000 

20 

20000 

precip (cm) 

15 

10 

15000 

Q (cfs) 

10000 

5 

5000 

0 

0 

1/Feb 

2/Feb 

3/Feb 

4/Feb 

5/Feb 

6/Feb 

7/Feb 

8/Feb 

9/Feb 

10/Feb 

11/Feb 

12/Feb 

13/Feb 

14/Feb 

15/Feb 

16/Feb 

17/Feb 

18/Feb 

19/Feb 

20/Feb 

21/Feb 

22/Feb 

23/Feb 

24/Feb 

25/Feb 

26/Feb 

27/Feb 

28/Feb 

San Benito Precip (cm) San Benito River at HWY 156 near Hollister Q (cfs) cumulative precip (cm) 

DRAFT 7/22/03 

53 


Precipitation data from California Irrigation Management Information System station 

#126 at San Benito (point 006 on map), available at: http://www.cimis.water.ca.gov/, accessed 

21 May 27, 2003. 

Stream discharge data from the U.S. Geological Survey for the San Benito River at 

HWY 156 near Hollister (point 007 on map), available at: 


egin_date=03/01/1995&end_date=03/31/1995&period=, accesses 27 May 2003. 

30 

Corralitos Creek Hydrograph & Corralitos Precipitation 1995 

1400.00 

25 

1200.00 

20 

1000.00 

precip (cm) 

15 

800.00 

600.00 

Q (cfs) 

10 

400.00 

5 

200.00 

0 

0.00 

30-Mar 

29-Mar 

28-Mar 

27-Mar 

26-Mar 

25-Mar 

24-Mar 

23-Mar 

22-Mar 

21-Mar 

20-Mar 

19-Mar 

18-Mar 

17-Mar 

16-Mar 

15-Mar 

14-Mar 

13-Mar 

12-Mar 

11-Mar 

10-Mar 

9-Mar 

8-Mar 

7-Mar 

6-Mar 

5-Mar 

4-Mar 

3-Mar 

2-Mar 

1-Mar 

Corralitos daily precip (cm) cumulative precip (cm) Corralitos Creek Q (cfs) 

DRAFT 7/22/03 

54 


50 

Corralitos Creek Hydrograph & Corralitos Precipitation 1998 

1200.00 

45 

40 

1000.00 

precip (cm) 

35 

30 

25 

20 

15 

800.00 

600.00 

400.00 

Q (cfs) 

10 

5 

200.00 

0 

0.00 

28/Feb 

27/Feb 

26/Feb 

25/Feb 

24/Feb 

23/Feb 

22/Feb 

21/Feb 

20/Feb 

19/Feb 

18/Feb 

17/Feb 

16/Feb 

15/Feb 

14/Feb 

13/Feb 

12/Feb 

11/Feb 

10/Feb 

9/Feb 

8/Feb 

7/Feb 

6/Feb 

5/Feb 

4/Feb 

3/Feb 

2/Feb 

1/Feb 

daily precip (cm) Q (cfs) cumulative precip (cm) 

Precipitation data from California Data Exchange Center for Corralitos (point 003 on 

map), available at: http://cdec.water.ca.gov/cgiprogs/selectQuerystation_id=COR&dur_code=H&sensor_num=2&start_date=2/1/95&end_date 

=2/28/95, accessed 28 May 2003. 

Stream discharge data from the U.S. Geological Survey for the Corralitos Creek (point 

001on map), available at: 


egin_date=02/01/1995&end_date=04/30/1995&period=, accessed 27 May 2003. 

DRAFT 7/22/03 

55 


APPENDIX 6: 

Topographic detail for a Cross Section in Appendix 5 Historical Change area 

Detailed topography of a section of lower San Benito River near Highway 101 

Appendix 6. A cross-section based on the December, 2000 aerial survey. Lower San 

Benito River just upstream from San Juan Road near Highway 101. Tilled bench at the lower left 

is 160 ft. elevation. Orchard is 142 ft elevation on old floodplain. Berm rises to between 154 and 

170 ft elevation. Thalweg of channel is at 130 ft elevation. Channel right bank is at 160 ft 

elevation. 

DRAFT 7/22/03 

56 


Figure 16 – San Benito River channel at Mitchell Road about one-half mile downstream 

(west) from the “new” Highway 156 bridge. The active channel is 1.0 km wide here. The banks 

here against the old floodplain are only 6-8 ft above the riverbed but that floodplain is now 

abandoned because the overwide channel accommodates all flow. Remnant floodplain is seen in 

the upper northeast and northwest corners and a small portion of the left bank at the bottom of 

the photo. Active bank cutting is toppling buildings along the right bank. Figs 8-10 (following) 

show how distinct floodplain and Lake San Benito terrace levels are at this point on the right 

bank. 

DRAFT 7/22/03 

57 


Fig 9: Lake San Benito “terrace” 

Fig 8: Recently abandoned active floodplain 

Fig 10. Abandoned floodplain surface 1 km north of Mitchell Road. Active channel on 

the left, Lake San Benito “terrace” on the right with power poles. View west, downstream. 

This is an example of easily recovered flood storage, now only 6-8 feet above the overwide 

(1 km) adjacent riverbed. 

DRAFT 7/22/03 

58 


Fig 15 Stream Barb Structures 

DRAFT 7/22/03 

59 


Appendix 3: Streambank Property Owners, San Benito River (see separate file) 

Appendix 7: Mines in the San Benito County Permit files, 2003 (see separate file) 

Appendix 8: Economic and Socioeconomic considerations 

Introduction 

Economic considerations for the Pájaro Watershed are almost as 

complex as the geological issues. Because the lower Pájaro Valley is cooled by 

fog in the summer, yet remains under marine influence all winter, the field 

survey crews recognized it in 1853-54 as an unusually favorable agricultural 

region (Wm. Johnson, 1854 US Coast Survey). High value crops can be grown 

and harvested all year in the rich Lake San Benito silt soils. Agricultural 

drainage tiles were installed at the beginning of the 20 th Century to enhance 

winter production in the lowermost part of the valley where waterlogging of soils 

could occur during the winter. By 1950 the flood-tolerant fruit tree and nut crops 

were being cut down in favor of much more valuable row crops. With the local 

selective breeding of berry varieties adapted to high production in morning fog 

sites, there was strong economic pressure to shift to very high value crops such 

as strawberries and cut flowers. 

Agriculture in the Lower Pájaro Valley is thus very different than in most 

agricultural areas of the world. In the Pájaro, it pays to tear down houses and 

parking lots and plant crops. Agricultural property has among the highest 

returns on investment as are found anywhere. This means that valuation of 

flood protection works cannot be treated as they would be for cropland in Iowa 

or Indiana. It further means that seasonal flooding of silt across fields, as is 

welcomed throughout most of the world, has a high cost to farmers in the 

Pájaro. Thus, cost-benefit analyses that must be accomplished for federal flood 

protection works have to be based on an entirely different metric than elsewhere 

in the United States. 

We attempted to disaggregate the Corps’ comparative cost figures for the 

scenarios that were released to the public as this report was being written. 

Despite repeated requests to the Corps’ offices in San Francisco, none of the 

lumped categories for cost assessment were provided to us. In no public 

meetings that we attended were these various cost categories explained or 

questioned. We thus cannot accurately estimate the cost-savings that are 

inherent in the upstream flood storage options presented here. 

But we take the position that however insubstantially based may be the 

Corps’ numbers, we can state that our cost estimate for a reduction of 4 feet in 

the height of the 100-year flood at Murphy’s Crossing in the Lower Valley is less 

costly. That is, the cost of the top 4-feet of flood protective works envisioned by 

the Corps’ in their scenarios is more expensive than our zero-public-cost 

upstream flood storage restoration alternative. 

DRAFT 7/22/03 

60 


Corps’ Data presented Alternatives By Ada Squires 2003 - Pájaro 

Estimates in millions 

raise levee 9 ft 

100 ft setback 

& raise 5 ft 

100 ft setback & 

raise 6 ft 

setback 

costs/ft. 

LERRD's 33.5 22.7 24.3 2.6 

Construction 193.7 130.7 131.7 1 

E&D, S&A 34.1 23 23.4 0.4 

Total Projected Cost 261.3 176.4 179.4 

Annual Cost 18 12.2 12.4 

OMRR&R 1.9 1 0.8 

Total Annual Cost 19.9 13.2 13.2 

Benefits 14.8 14.9 14.8 

Net Benefits -5.1 1.7 1.6 

Benefit: Cost 0.74 1.13 1.12 

Non-Federal Cost (25%) 44.1 44.1 44.9 

Squires Table 

Socioeconomic Context: 

The two areas where floodwater from the Pájaro River most affects 

communities are at the town of Pájaro and the city of Watsonville. Located near 

the mouth of the Pájaro River, these two communities are built where the Pájaro 

River is confined to an unnatural and unstable artificial flood channel. 

The upper watershed of the Pájaro River, which consists of over 90% of 

the watershed, is comparatively wealthy. San Benito County has a per capita 

income of $20,932/year with a poverty rate for families of 8.6%. Santa Clara 

County fares even better with a per capita income of $32,795/year with a 

poverty rate of 6.8%. 

When one compares those figures to that of Pájaro and Watsonville, one 

can easily see why the voices of those towns might not be heard in the politics 

of the watershed. The US Census Bureau reports that Pájaro has a per capita 

income of $9893/year, while 20.4% of its families are below the poverty level. 

The city of Watsonville has a per capita income of $13,205/year and a poverty 

level of 19.7%. It is important to note that these figures are those of the Census 

Bureau and do not accurately reflect the true populations in these cities due to 

migrant and illegal farm workers. In a survey of Monterey County and Santa 

Cruz County farm workers, the median family income was $11,000/year and 

$14,000/year respectively (Monterey County Farm Workers, 2003). 

In addition to low-income status, populations with a high percentage of 

minorities have historically borne the heavier weight of environmental problems 

than those with a higher percentage of Caucasians (Bullard, pg.xv). The state 

of California has a Caucasian population consisting of 46.7% of the total 

DRAFT 7/22/03 

61 


population. San Benito County is 46% Caucasian, while Santa Clara County is 

44% Caucasian. The City of Watsonville is only 24.9% Caucasian (75.1% 

Hispanic) and the town of Pájaro is a mere 3.7% Caucasian (94.2% Hispanic). 

Both the towns of Watsonville and especially Pájaro, which was 

evacuated during the flood of 1995 and again in 1998, are strongly affected by 

flood risk. Families are struggling to live day to day, and another large flood 

could devastate their livelihood. 

Per Capita Income($) 

% of Pop. Caucasian 

Pájaro 9893 Pájaro 3.7 

Watsonville 13,205 Watsonville 24.9 

Santa Clara Cnty 32,795 Santa Clara Cnty 44 

San Benito Cnty 20,932 San Benito Cnty 46 

California 22,711 California 46.7 

Poverty Level - Families 

% of Pop. Hispanic 

Pájaro 20.4 Pájaro 94.2 

Watsonville 19.7 Watsonville 75.1 

Santa Clara Cnty 6.8 Santa Clara Cnty 24 

San Benito Cnty 8.6 San Benito Cnty 47.9 

California 15.3 California 32 

US Census Data Table 

DRAFT 7/22/03 

62 













Lani Clough 



Joy Larson 


Steve Mack 


Serena Pring 

Emily Roth 

Amy Thistle 


References A62 Draft of July 22, 2003

References Cited: 

Ackers and Charlton, 1970, Meander Geometry Arising from Varying Flows. Jour. Hydrol, v. XI, 

no. 3, p 230-252 in U. S. Army Corps of Engineers, Engineering Manual (EM) 1110-2- 

1418 : Channel Stability Assessment for Flood Control Projects, 1994 

Anderson, R.S., (1990) Evolution of the northern Santa Cruz Mountains by advection of crust past 

a San Andreas Fault bend. Science 249: 397-401. 

Bullard, R., 1994, Unequal Protection: Environmental Justice and Communities of Color. Sierra 

Club Books. San Francisco, Ca. 

Calciano, Elizabeth, 1967, The Pájaro Valley apple industry, 1890-1930. An interview oral 

history. 

California Historical Survey Commission, 1923, California county boundaries: a study of the 

division of the state into counties and the subsequent changes in their boundaries. 

Berkeley 

Crosetti, J.J., 1993 : Pájaro Valley agriculture, 1927-1977 / interviewed and edited by Randall 

Jarrell. Oral history Collections, UC Santa Cruz 

Curry, R. R., 1981, Watershed Form and Process: The Elegant Balance. Chapter. 20 (p. 319- 

340) in Emery, F.E. (ed), “Systems Thinking”, Vol. 2, Penguin Books, Middlesex, 

England, 474 p. Penguin Modern Management Readings, Education Series, published 

simultaneously by Penguin Books, New York; etc. 

Curry, R. R., 1996, Coupling Marine and Terrestrial Watershed Processes. NOAA, Monterey 

Bay National Marine Sanctuary Symposium, 

http://bonita.mbnms.nos.noaa.gov/sitechar/sympcurr.html 

Farquhar, Francis P., 1930, Up and down California in 1860-1864. The journal of William H. 

Brewer. Princeton, Yale University Press, p. 152. 

Federal Emergency Management Agency (FEMA), 1996, FEMA Flood Map for San Benito 

County (digital copy) 

__________, 2002, Guidelines and Specifications for Flood Hazard Mapping Partners: Appendix 

C: Guidance for Riverine Flooding Analysis and Mapping. Final. 

Goldner Associates, 1997, report to San Benito County Planning Dept. 

Iwamura, T.I., 1995, Hydrogeology of the Santa Clara and Coyote Valleys groundwater basins, 

California, in Sanginés, E.M., Andersen, D.W., and Buising, A.B., eds., Recent geologic 

studies in the San Francisco Bay area: Los Angeles, Society of Economic Paleontologists 

and Mineralogists, Pacific Section Guidebook, v. 76, p. 173–192. 

Jenkins, Olaf P., 1973, Pleistocene Lake San Benito, California Geology, July 1973, Vol. 26, No. 

7. 

Jones & Stokes Associates, 1998, Groundwater Management Plan for the San Benito County 

Part of Gilroy-Hollister Groundwater Basin – for San Benito County Water District 

Kilburn, C., 1972, Groundwater hydrology of the Hollister and San Juan Valleys, San Benito 

County, California. 1913-1968. USGS Open File Report 73-144, Sacramento, CA 

Monterey County Survey of Farm Workers. 

http://www.co.monterey.ca.us/dss/affiliates/downloads/farmworker_survey/7_Work_Issue 

s.pdf 

Riley, Ann L. , 2003, A Primer on Stream and River Protection for the Regulator and Program 

Manager. California Regional Water Quality Control Board, San Francisco Bay Region, 

Tech. Ref. Circular W.D. 02-#1 

Rosgen, Dave, 1996, Applied River Morphology. Wildlife Hydrology, Pagosa Springs, CO 

Secretary of War, 1944, Pájaro River, Calif. [microform] : letter from the Secretary of War 

transmitting a letter from the Chief of Engineers, United States Army, dated December 

13, 1943, submitting a report ... authorized by the Flood Control Acts approved on June 

22, 1936, and August 28, 1937. Washington, D.C. : U.S. G.P.O., 1944. 

Secretary of the Army, 1966, Pájaro River Basin, California : letter from the Secretary of the 

Army, transmitting a letter form the Chief of Engineers, Department of the Army, dated 

August 27, 1965, submitting a report, together with accompanying papers and 

DRAFT 7/22/03 

63 


. 

illustrations, on an interim report on the Pájaro River Basin, California, requested by a 

resolution of the Committee on Flood Control, House of Representatives, adopted May 

14, 1945 Washington : U.S. G.P.O. 

Stanley, Richard G., Robert C. Jachens, Paul G. Lillis, Robert J. McLaughlin, Keith A. 

Kvenvolden, Frances D. Hostettler, Kristin A. McDougall, and Leslie B. Magoon, 2002, 

Subsurface and Petroleum Geology of the Southwestern Santa Clara Valley 

(“Silicon Valley”), California. USGS Professional Paper 1663. 

United States. Army. Corps of Engineers. Committee on Channel Stabilization. 1998, Channel 

stability problems, Pájaro River, Watsonville and Pájaro, California : U.S. Army 

Engineer Committee on Channel Stabilization report of the 63th meeting / by Ronald R. 

Copeland and Dinah N. McComas, editors ; prepared for U.S. Army Corps of Engineers. 

94 p. : ill. ; 28 cm. — (ERDC/CHL ; SR-00-3)(CCS ; 00-1) 

US Census Bureau. http://factfinder.census.gov/servlet/AdvSearchByPlaceServlet 

U.S. Geological Survey, Interagency Advisory Committee on Water Data, 1982, Guidelines for 

determining Flood Flow Frequency, Bull #17B. 

Whiting, Peter J, 1998, Floodplain Maintenance Flows, pp. 160-170 in Rivers, v. 6, no. 3 

Historical materials reviewed 

1853. US Coast Survey. Part of the Coast of California from the Pájaro River Northward. T- 

4442 1:10,000. UCSC Map Library. (including field notes) 

1854. US Coast Survey. Part of the Coast of California from the Pájaro River Southward. T-473. 

1:10,000. UCSC Map Library . (including field notes) 

1858. John Wallace. Plat of the Rancho Bolsa del Pájaro . 1:15,840. UCSC Map Library. 

1865. Fuller, A.D. Map of a part of the Rancho Bolsa del Pájaro . 1:2,400. UCSC Map Library. 

1912. USGS Capitola Quadrangle. 1:62,500. Surveyed in 1911-12. UCSC Map Library. 

1917. USGS. San Juan Bautista Quadrangle. 1:62,500. Surveyed in 1915. UCSC Map Library. 

1921 . USGS, Hollister Quadrangle: 1:62,500 Surveyed in 1917-1919, UCSC Map Library 

1930 . Lloyd Bowman, the Santa Cruz County Surveyor. Plan and profile of the Pájaro River. 

1:2,400. 13 sheets (Santa Cruz County Surveyors Office). 

1931 aerial photographs of the Pájaro Valley, from the Fairchild Collection at Whittier College. 

UCSC Map Library 

1938. City of Watsonville Plan and sections, Pájaro River and levees. 1:1,200. 2 sheets. 

1949 US Army Corps of Engineers. Plan of Construction (As-Built), Pájaro River Levee Project. 

With maintenance manual 

"San Benito" Monterey County 1843. (Rancho San Benito) Terreno de San Juan Bautista 

concedido a Don Augustin Narvaes por El Gobernador Micheltoreno : [Santa Clara Co., 

Calif.] / Medido por C.S. Lyman ; y Sherman Day Published 1850 Scale Scale [ca. 

1:16,000] 

Deseño del Rancho de San Juan Bautista : [Santa Clara County, Calif.] Published [184-] Scale 

Scale [ca. 1:33,000] (W 121°53/N 37°17) 

DRAFT 7/22/03 

64 


APPENDIX 3 Streambank Property Owners along the San Benito River below Tres Pinos 

http://home.csumb.edu/c/currybob/world/Pajaro/Appendix%203.htm 

Page 1 of 2 

6/7/2011 


P jaro 

River Holstr = Hollister Watershed 

S.J. = San Jose Spring 2003 

Contacts S.J.B. =San Juan Bautista Steve Mack 

Glry = Gilroy 

Cmrilo = Camarillo 

Slnas = Salinas 

Oxnrd = Oxnard 

Bookpageparcel 

# Owner Acres Address Phone Nearest Cross Street 

020-28-41 Brigantino J-V Trust 28.69 150 San Felipe Rd. Holstr 831-637-5563 Hospital Rd. 

020-28-13 Lemos Family Trust 27.96 320 Ladd Ln. Holstr 831-636-9838 Union Rd. 

020-28-12 Granite Rock #29381 (Jim West) 9.06 Cienega 

020-28-46 Felice Family Living Trust 10.2 2220 Cienega Rd. Holstr 831-638-1198 Cienega 

020-28-47 Felice Family Living Trust 17.9 2220 Cienega Rd. Holstr Cienega 

021-10-4 Granite Rock #29381 (Jim West) 3 Cienega 

021-10-3 Granite Rock #29381 (Jim West) 34.21 831-768-7071 Cienega 

021-10-12 Hollister School District 1.09 Cienega/ Union School 

021-10-17 County of San Benito 19.63 Cienega/ Summerset 

020-17-17 Palmtag Frances Trustee 22.59 1570 Cienega 831-637-3175 Cienega/ Eastview 

020-17-14 Felice Family Living Trust 13.3 2220 Cienega Rd. Holstr 831-638-1198 Cienega/ Eastview 

020-16-14 Granite Rock #29381 (Jim West) 27.88 Nash 

020-16-15 Granite Rock #29381 (Jim West) 24.46 Nash 

020-16-16 Escover Manuel J- Joyce 1.25 315 Riverside Rd. Holstr 831-637-2915 Nash 

020-06-42 Sandman INC (Star Concrete) 35.85 1510 S. 7th St. S.J. Nash 

020-06-43 Sandman INC (Star Concrete) 6.01 1510 S. 7th St. S.J. Nash 

020-06-30 Schipper Properties 1.57 2984 Monterey Rd. S.J. Nash 

O'Connell Ranch (Cal LTD 

013-12-11 Liability) 79.1 P.O. Box 58 S.J.B. Bolsa Rd. 

013-12-06 Breen Elizebeth H- Patrick 71.2 1439 San Benito St. Holstr 831-637-5469 San Benito River 

012-07-02 Breen Elizebeth H- Patrick 96.09 1439 San Benito St. Holstr San Justo Rd. 

012-07-01 Breen Elizebeth H- Patrick 247.69 1439 San Benito St. Holstr San Justo Rd. 

012-08-02 

Gubser Survivors Trust (Dorris 

G.) 100 7800 Miller Ave. Glry San Justo Rd./ Lucy Brown 

012-08-03 Hudner Philip-Stephen (J. Breen) 56.56 1439 San Benito St. Holstr San Justo Rd./ Lucy Brown 

018-10-21 Granite Rock #29381 (Jim West) 22.74 Mitchell Rd./ Freitas 

018-10-31 Stevens Family Trust 33.43 564 4th St. Holstr Mitchell Rd./ Freitas 

018-10-33 Bonnie Brae Co (Felice L. Phillip 22.24 P.O. Box 1356 Holstr Mitchell Rd./ Freitas 

018-10-29 Granite Rock #29381 (Jim West) 20.83 Mitchell Rd./ Freitas 

018-10-02 Granite Rock #29381 (Jim West) 29.51 831-768-7071 Mitchell Rd./ Freitas 

5415Santa Clara Ave. 

018-10-22 Grether Enterprises 92.058 Cmrilo 

Flint Rd. 

5415Santa Clara Ave. 

018-09-13 Grether Enterprises 119.77 Cmrilo 

Flint Rd. 

018-09-24 Granite Rock #29381 (Jim West) 13.13 BixbyRd. / Duncan 

018-09-15 Granite Rock #29381 (Jim West) 10.7 BixbyRd. / Duncan 

018-09-17 Schipper Properties 4.68 2984 Monterey Rd. S.J. BixbyRd. / Duncan 

018-09-20 Schipper Properties 12.23 2984 Monterey Rd. S.J. BixbyRd. / Duncan 

018-09-19 Granite Rock #29381 (Jim West) 36.97 831-768-7071 BixbyRd. / Duncan 

018-09-18 Brookhollow Ranch L P 10.16 P.O. Box 68 Holstr BixbyRd. / Duncan 

018-08-04 Black Daniel L- Teresa M 8.2 1240 Bixby Rd. S.J.B. 831-623-2742 Duncan Rd./ Bixby 

018-08-21 Brookhollow Ranch L P 13.08 P.O. Box 68 Holstr Duncan Rd. 

018-08-20 Freitas Joseph 23.66 700 Duncan Ave. SJB 831-623-4444 Duncan Rd. 

018-08-25 Wright Roberta-Martha 9.94 5380 Poppy Blossom Ct. SJ Duncan Rd. 

018-08-24 Freitas Bernard Family Trust 9.94 8061 Fairview Rd. Holstr Duncan Rd.


http://home.csumb.edu/c/currybob/world/Pajaro/Appendix%203.htm 

Page 2 of 2 

6/7/2011 

018-08-23 Frietas Lucille M in Trust 25.62 801 Olympia Ave. SJB 831-623-4246 Duncan Rd./Lucy Brown ln. 

018-08-22 

Frietas Lawrence & A Family 

Trust 21.64 771 Olympia Ave. SJB 831-6234303 Duncan Rd. 

018-08-07 Foster Philip W- Katherine 29.89 P.O. Box 249 SJB Duncan Rd. 

018-08-06 S.B. Nursery (Delaware LTD Co) 29.81 P.O. Box 4070 Slnas Duncan Rd. 

2700 Camino Del Sol. 

018-08-05 Seminis Vegetable Seed 29.89 Oxnrd 

Duncan Rd./Lucy Brown ln. 

018-08-01 Breen Elizebeth H- Patrick 16.31 1439 San Benito St. Holstr 831-637-5469 Duncan Rd. 

018-07-01 Freitas Bernard Family Trust 19.862 8061 Fairview Rd. Holstr San Justo Rd. / Lucy Brown 

018-06-26 Granite Rock #29381 (Jim West) 27.08 Buena Vist Rd. 



018-06-12 Granite Rock #29381 (Jim West) 6 Buena Vist Rd. 


018-05-11 Granite Rock #29381 (Jim West) 247.95 831-768-7071 Buena Vist Rd. 

018-05-08 Brookhollow Ranch L P 23.96 P.O. Box 68 Holstr Brookhollow Rd. 

018-05-07 Brookhollow Ranch L P 22.67 P.O. Box 68 Holstr Brookhollow Rd. 

018-05-06 Breen Elizebeth H- Patrick 62.32 1439 San Benito St. Holstr 831-637-5469 

Buena Vist Rd./ 

San Benito River

Historical Change in San Benito River east of Hwy 101 

Plate 39: Top photo, December 2000; bottom photo, June 1939 

See Appendix Plate XX for topographic maps of this site. River flow is from right to left. 

Overbank floodplain areas are clearly visible in 1939, as is a wide aggrading sand-filled channel. Mining 

beginning in the 1940’s has now lowered the channel 15-20 feet or more to intersect groundwater. An 

incised channel can be seen in the vegetated mined-out area today. Some areas of original flood plain 

in 1939 are now occupied by industrial development along Highway 101 and along San Juan Highway 

north of Anzar High School.

Historical Change in San Benito River Just above Hwy 101 

Portions of San Juan Bautista and Chittenden 1:24,000 topographic quadrangles showing 1952 

topography with mining that was interpreted as active in 1997-98. The purple overprint convention 

differs between the two matched maps, but streambed alteration is indicated over most of the original 

channel area. 

Topography based on the December 2000 photobase. Levees isolate active channel from both 

historic and newly excavated floodway. See text for details.

Pájaro River Watershed Flood Protection Plan - The Pajaro River ...

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