CVPIA – Annual Report for Fiscal Year 2004 

1 

Implementation of the 

Central Valley Project Improvement Act 

Annual Report for Fiscal Year 2004 

U.S. Department of the Interior 

Fish and Wildlife Service 

Bureau of Reclamation 

July 2005
CVPIA – Annual Report for Fiscal Year 2004 2 

Contents 

INTRODUCTION.....................................................................................................................................4

The Central Valley Project's Role in California's Water Resources ..............................................4

The CVPIA Mandate...........................................................................................................................5

IMPLEMENTING THE CVPIA..............................................................................................................6

Process...................................................................................................................................................6

Priorities................................................................................................................................................7

The Focus and Priorities for Anadromous Fish ....................................................................8

The Focus and Priorities for Refuges and Waterfowl...........................................................9

The Focus and Priorities for Other Fish and Wildlife and Associated Habitats.............10

Coordination ......................................................................................................................................11

Funding Sources ................................................................................................................................11

FISCAL YEAR 2004 ACCOMPLISHMENTS.....................................................................................15

Project Title: Anadromous Fish Restoration Program.....................................................15

Project Title: Evaluation of Anadromous Fish Instream Flow Needs...........................21

Project Title: Habitat Restoration Program .......................................................................22

Project Title: San Joaquin River Riparian Habitat Restoration Program ......................23

Project Title: Management of Dedicated CVP Water for Environmental Purposes....25

Project Title: Water Acquisition Program .........................................................................27

Project Title: Tracy Pumping Plant Mitigation Program ................................................28

Project Title: Contra Costa Canal Pumping Plant Fish Screen Project..........................29

Project Title: Flow Fluctuation/Reservoir Storage Management Program..................30

Project Title: Red Bluff Diversion Dam Fish Passage Program......................................30

Project Title: Clear Creek Restoration Program ...............................................................31

Project Title: Spawning Gravel Replenishment Program ...............................................32

Project Title: Comprehensive Assessment and Monitoring Program...........................34

Project Title: Glenn-Colusa Irrigation District Fish Screen Replacement Project ........35

Project Title: Anadromous Fish Screen Program .............................................................35

Project Title: Trinity River Restoration Program..............................................................36

Project Title: Refuge Water Supply Program – Water Conveyance Component ........38

Project Title: Refuge Water Supply Program – Facilities Construction Component ..39

Project Title: Refuge Water Supply Program – San Joaquin Basin Action Plan 

Component .....................................................................................................40

Project Title: Ecosystem/Water System Model Development Program.......................41

Project Title: Land Retirement Program............................................................................42

DISCUSSION OF CVPIA IMPLEMENTATION AND RESULTS ...............................................45

Anadromous Fish - Biological Response..............................................................................46

Refuges and Waterfowl – Biological Response ...................................................................49

Other Fish and Wildlife – Accomplishments.......................................................................50

CONCLUSIONS .....................................................................................................................................51
CVPIA – Annual Report for Fiscal Year 2004 3 

FIGURES 

1 - CVPIA Expenditures by Fund Source – Fiscal Years 1993-2004 ......................................... 13 

2 CVPIA Expenditures by Fund Source – Fiscal Year 2004 .................................................... 13 

3 - Total CVPIA Expenditures by Action Category – Fiscal Years 1993-2004......................... 14 

4 - Total CVPIA Expenditures by Action Category – Fiscal Year 2004.................................... 14 
CVPIA – Annual Report for Fiscal Year 2004 4 

Central Valley Project Improvement Act 

Annual Report for Fiscal Year 2004 

INTRODUCTION 

In one of its last actions of the session, the 102nd Congress in 1992 passed, and the President 

signed, the multi-purpose water legislation known as the Central Valley Project Improvement 

Act (CVPIA or Act). Officially designated Title 34 of Public Law 102-575, this landmark piece of 

legislation mandates changes in the purposes and management of the Bureau of Reclamation’s 

(Reclamation) Central Valley Project (CVP) and specifically focused the Secretary of the 

Department of the Interior (Interior) on protection, restoration and enhancement of fish and 

wildlife associated with the CVP. The Secretary, in turn, assigned primary responsibility for 

implementing CVPIA’s many provisions to Reclamation and the U.S. Fish and Wildlife Service 

(Service), both agencies of Interior. 

It has been 12 years since Congress passed the CVPIA and, during that period, Reclamation and 

the Service have been diligently implementing its many provisions. Many have been completed 

and most others are well under way, at a cost so far of more than $759.4 million of State, Federal 

and private funds. Significant progress has been made in accomplishing the mandates that 

Congress established. While Interior is rightly proud of its accomplishments to date, additional 

time, effort, and funds will be needed to fulfill the CVPIA’s requirements and to achieve all of 

the goals and objectives embodied in the statute. This report is intended as a summary of the 

actions taken by Reclamation and Service personnel, working together with other State and 

Federal agencies and numerous partners and stakeholders, in fiscal year (FY) 2004. Greater 

detail on the programs and projects described here, or on the progress towards achieving the 

Act’s goals and objectives, can be obtained by contacting either agency or the individual CVPIA 

project and program managers directly. 

The Central Valley Project's Role in California's Water Resources

For almost 70 years, California has depended on the CVP for a large part of its water needs, 

particularly for agriculture. With a climate typified by extremely variable precipitation, both 

temporally and regionally, the State relies heavily on dams and reservoirs to balance and 

manage its water resources, and on an extensive distribution system to match water supplies 

with regional needs. 

Much of the State's water originates in the north and is conveyed southward, primarily through 

the Sacramento River system. Some water is diverted along the way, and the rest flows into the 

Sacramento-San Joaquin River Delta (Delta), where CVP water co-mingles with other supplies 

such as those of the State Water Project (SWP). About half of the water entering the Delta is 

pumped south: the remainder discharges to the San Francisco Bay and Pacific Ocean. Because 

of the way water is captured and moved through the Central Valley system, the CVP affects, 

and is affected by, the many unresolved water issues in California involving ecosystem balance 

in its river systems and the Delta. 
CVPIA – Annual Report for Fiscal Year 2004 5 

The sensitive ecosystems of the Central Valley, the Delta estuary, San Francisco Bay, and the 

Trinity River are affected by water diversions, particularly in drought years, so much so that the 

courts have intervened to assure that adequate fresh water enters these systems. Compliance 

with Endangered Species Act (ESA) and water quality requirements mandates releases from 

CVP dams to regulate water temperatures, salinity, and instream flows, and limits water 

diversions to protect listed fish from the effects of pumping. These factors have greatly 

increased the competition for existing supplies and have focused scrutiny on the ways that 

water resources are being used. 

Conditions have greatly changed since the CVP was authorized in 1935. Population growth 

and development have increased farm, urban, and industrial water demands. Concurrently, 

stocks of fish and wildlife have declined, resulting in some species being listed as endangered 

or threatened due to severe habitat loss. In response, a new imperative for resource 

management and ecological stewardship has evolved. 

The CVPIA Mandate 

The intent of Congress in passing the 

CVPIA is contained in Section 3402. 

Congress, recognizing the importance of the 

CVP in California’s water resources picture, 

made significant changes in the policies and 

administration of the project – more than 

any other legislation in the CVP’s almost 70-

year history. The Act also redefined the 

CVP’s purposes and identified several 

specific goals and objectives for Interior to 

meet. 

To achieve the CVPIA’s purposes, a large 

number of provisions were incorporated 

into the statute. These include specific 

programs, measures, and operational and 

management directives, all to be 

implemented consistent with the 

requirements of California and Federal law. 

These provisions deal with water contracts, 

improved water management, restoration of 

anadromous fish populations, water 

supplies for State and Federal refuges and 

wildlife habitat areas, mitigation for other 

CVP-impacted fish and wildlife, and 

retirement of drainage-impaired 

agricultural lands. They also provide for 

system-wide modeling, numerous 

investigations and studies, and for monitoring to assess the biological results and effectiveness 

of CVPIA actions. To help implement these measures, the Act provided for establishing a 

Purposes of the CVPIA (Section 3402)

(a) to protect, restore, and enhance fish, wildlife, 

and associated habitats in the Central Valley 

and Trinity River basins of California; 

(b) to address impacts of the Central Valley 

Project on fish, wildlife, and associated 

habitats; 

(c) to improve the operational flexibility of the 

Central Valley Project; 

(d) to increase water-related benefits provided 

by the Central Valley Project to the State of 

California through expanded use of voluntary 

water transfers and improved water 

conservation; 

(e) to contribute to the State of California’s 

interim and long-term efforts to protect the 

San Francisco Bay/Sacramento-San Joaquin 

Delta Estuary; and 

(f) to achieve a reasonable balance among 

competing demands for use of Central Valley 

Project water, including the requirements of 

fish and wildlife, agricultural, municipal and 

industrial, and power contractors
CVPIA – Annual Report for Fiscal Year 2004 6 

Restoration Fund, derived from fees paid by those who have benefited from the CVP’s water 

and power supplies. 

The CVP and other water projects have helped make the Central Valley the richest agricultural 

region in the nation and support the largest population of any state in the nation. California 

leads the nation in water use, both surface water and groundwater. The ability to develop and 

use this precious resource has been a boon to the economy of the State but has also come at 

great price to the natural environment. The CVPIA has afforded Interior a prime opportunity to 

help restore conditions favorable for fish and wildlife in the Central Valley while at the same 

time providing for the continuation of its rich agricultural heritage and service to municipal and 

industrial users throughout the State. 

IMPLEMENTING THE CVPIA 

Process

Upon the CVPIA’s passage, Reclamation and the Service immediately focused on three main 

fish and wildlife restoration initiatives identified in the Act. One of the most ambitious of these 

was to make all reasonable efforts to at least sustainably double the natural production of six 

species of anadromous fish, species believed to have been affected by CVP construction and 

operation. The process to determine the reasonableness of anadromous fish restoration actions 

was defined in the Final Restoration Plan (Plan) for the Anadromous Fish Restoration Program 

(AFRP; 2001). 

Actions contained within the Plan were 

determined to be reasonable given 

numerous technical, legal, and 

implementation considerations. The 

diagrammatic explanation to the right is 

excerpted from the Plan and depicts the 

process used to determine if actions 

were reasonable. 

Another restoration initiative was to 

supply much-needed water to Federal 

and State refuges and other migratory 

waterfowl habitats in the Central Valley. 

The third was to address other adverse 

environmental impacts of the CVP, 

impacts not previously offset or 

specifically covered in other provisions 

of the Act. At the same time, Interior 

reaffirmed its commitment to improving 

the operational flexibility of the CVP in 

order to more effectively balance and 

meet the many competing demands for 

 action

1) Would the action benefit natural 

production of anadromous fish in a 

manner consistent with the provisions 

and intent of the CVPIA?

no

yes

2) Have the key technical and scientific 

issues been resolved and does the 

action comply with applicable laws and 

regulations?

3) Does the CVPIA specifically 

authorize and direct Interior to 

implement the action, and can it be 

implemented without a partner?

5) Has the interested public shown 

sufficient support to suggest a partner 

will be identified in the future?

no

Action considered reasonable 

inclusion in the Restoration Plan

yes

6) Either resolve technical, 

scientific, legal, or partnership 

issues and reconsider the 

revised action or eliminate the 

action from further 

consideration.

4) Is the action supported by all partners 

necessary to implement the action?

yes

no

yes

no

no

yes

Refer to other 

programs for 

implementation

 restoration

Proposed
CVPIA – Annual Report for Fiscal Year 2004 7 

project water supplies, including environmental, agricultural, municipal and industrial, and 

power generation needs. 

Procedural policies and guidelines were also developed for implementing the Act’s specific 

provisions. Actions proposed for implementation under the CVPIA are prioritized on an 

annual basis. Any action undertaken to implement the Act must be designed to contribute to 

the attainment of CVPIA goals while providing the greatest public benefit and minimizing 

adverse impacts to other CVP beneficial uses. Great emphasis is placed on forming 

partnerships and coordinating with other restoration efforts planned or already underway 

throughout the Central Valley. Stakeholders and the public are to be fully involved and kept 

informed. Another key procedural objective is to use the funds available to us in a cost-effective 

manner. 

Most of the programs established to address specific CVPIA provisions had the same initial 

steps in common. All required an administrative structure, opportunity for public and 

stakeholder involvement, and coordination with potential partners to develop program plans. 

Compliance with applicable State and Federal laws before initiating action was essential. There 

were large differences in the amount of time and effort required to complete these steps for the 

various programs, primarily dependent upon the relative complexity of the issue and degree of 

public interest or controversy. For some provisions of the Act, plans were developed and 

implemented within the first year while, for others, plans are still being completed. 

For planning and budgeting purposes, we 

have classified all CVPIA actions into one of 

eight action categories. We use these 

categories to summarize our activities in 

CVPIA reports, in discussions with the public 

and stakeholders, many who are interested in 

only certain facets of CVPIA implementation, 

and in coordinating with potential partners 

with interests in specific topic areas. Most of 

these eight categories involve several 

individual programs and related actions. 

Priorities

Several factors are considered in establishing priorities for CVPIA actions. These include the 

importance of the action to achieving CVPIA program goals; its readiness or the amount of 

additional planning needed to implement the action; its cost effectiveness; and the availability 

of funding. Many provisions of the Act require plans or studies prior to taking action. In 

addition, administrative requirements, such as compliance with various State and Federal laws, 

must be undertaken before measures can be implemented. Finally, because the Act had specific 

compliance dates for some provisions, implementation was responsive to the prescribed dates. 

Most of the CVPIA’s provisions, however, have allowed us the discretion to implement in a 

purposeful, proactive manner those measures and programs deemed most important, most 

CVPIA Action Categories

 Administrative Processes 

 Contracting and Improved Water 

Management 

 Anadromous Fish – Habitat 

Restoration 

 Anadromous Fish – Structural 

Measures 

 Refuges and Waterfowl 

 Other Fish and Wildlife Resources 

 Studies, Investigations, and Modeling 

 Monitoring
CVPIA – Annual Report for Fiscal Year 2004 8 

urgent, or that would result in the greatest or most immediate benefit. This is especially true for 

the Act’s fish and wildlife provisions. To help prioritize our efforts for fish and wildlife over the 

short-term, we have used a biological “focus area” approach that takes into account three 

parameters: 

1. Species or populations of greatest concern; 

2. Controllable factors that have the greatest influence on these species or populations; and 

3. Geographic areas or habitats in most critical need of help for the priority species and/or 

for the greatest number of species. 

Other biological considerations and principles applied in our implementation of the CVPIA 

include the emphasis in the Act itself on restoration of natural habitat components and 

ecosystem function and viability. Another is the emphasis on “focused packages” (suites of 

actions similar in nature in a specific geographic area) of projects to maximize and accelerate 

biological benefits in key geographic areas or watersheds instead of implementing measures in 

a scattered fashion over a wide geographic area. Critical non-biological principles include the 

technical feasibility and readiness of measures for 

implementation, and the support and availability of partners 

and funding to implement certain measures. 

The Focus and Priorities for Anadromous Fish. The 

CVPIA [Section 3406(b)(1)] directed us to develop and 

implement a program that makes all reasonable efforts to 

double, by the year 2002, the “natural” production of six 

species of anadromous 

fish in Central Valley 

rivers and streams over 

average levels that 

existed between 1967 

and 1991. The majority 

of the other measures 

and programs in Section 

3406(b) were intended 

to contribute to that 

effort. 

Using the biological focus approach, the Delta has been 

determined to be one of the highest priority geographical areas 

for anadromous fish. The Delta has been highly altered by 

water resource development projects and operations. Still, all 

species and races of anadromous fish must pass through the 

Delta, both as adults moving upstream and as juveniles on 

their way to San Francisco Bay and the open ocean. In doing 

so, they pass close to and are greatly affected by the operation 

of water supply project facilities. The opportunity for 

Species of Anadromous Fish

To Re Restored Under CVPIA

• Chinook salmon (all races) 

• Steelhead 

• Striped bass 

• American shad 

• White sturgeon 

• Green sturgeon
CVPIA – Annual Report for Fiscal Year 2004 9 

implementing measures in the Delta having widespread beneficial effects for all anadromous 

fish is tremendous. Emphasis there has been on increasing streamflows and reducing water 

diversions during peak periods in the out-migration of juvenile anadromous salmonids and 

when other threatened or endangered species, such as the delta smelt, are in the vicinity of the 

diversion pumps. Other operational changes and structural measures to enhance conditions 

during out-migration are also being employed. 

The east-side tributaries of the Sacramento River are another major focus area for anadromous 

fish, in particular Butte, Deer and Mill creeks and, to a lesser extent, Big Chico Creek. These 

streams support the last significant runs of the threatened spring-run Chinook salmon. Once 

the most numerous race in the valley, the spring-run had dwindled to less than 2,000 fish in 

1991. Dams have blocked access to the headwater areas of streams that once constituted their 

natural habitats, and flows needed to provide pools of cool water for them to survive over the 

summer (they migrate into the streams in spring and delay spawning until the fall) have been 

diverted. Restoration actions on these streams have emphasized the acquisition of water for 

instream flow, laddering or removal of dams and other impediments to migration, screening or 

removal of diversions, and acquisition and restoration of riparian habitats that provide relief 

from solar heating of the stream channel and woody debris and nutrients to the aquatic 

ecosystem. 

Other Sacramento River tributaries, most notably Battle Creek, Clear Creek, Antelope Creek, 

and the Yuba River, have also been targeted for restoration efforts. Along with Deer, Mill, and 

Butte creeks, these streams support naturally spawning populations of steelhead, another listed 

threatened species. Juveniles of this species generally spend a year or more in their natal 

streams. Consequently, they are subject to many of the same limiting factors as the spring-run 

Chinook salmon, most notably the need to access the cooler upper reaches of streams and 

adequate supplies of summer water. Restoration efforts on these streams have focused on the 

same types of measures as for the spring-run Chinook on Butte, Deer, and Mill creeks. 

The Focus and Priorities for Refuges and 

Waterfowl. With the decline of natural wetlands 

in the Central Valley, wildlife specialists have 

been forced to intensively manage the remaining 

300-400,000 acres of wetlands to accommodate 

the millions of wintering waterfowl, shorebirds, 

and other wetland-dependent wildlife that 

depend on them for survival. This has entailed 

careful management of limited and uncertain 

water supplies to provide for only the most 

critical of needs for a limited number of species. 

Some very difficult trade-offs of one species for 

another was the rule rather than the exception. 

With the CVPIA’s passage, we were directed to 

make available the water supply needed for full 

habitat development at specific Central Valley 

State and Federal refuges and private wetland 

Central Valley Refuge Areas 

Receiving CVPIA Water

• Sacramento National Wildlife Refuge 

• Delevan National Wildlife Refuge 

• Colusa National Wildlife Refuge 

• Sutter National Wildlife Refuge 

• Gray Lodge Wildlife Area 

• North Grasslands Wildlife Area 

• San Luis National Wildlife Refuge 

• Volta Wildlife Area 

• Merced National Wildlife Refuge 

• Los Banos Wildlife Area 

• Grassland Resource Conservation District 

• Mendota Wildlife Area 

• Pixley National Wildlife Refuge 

• Kern National Wildlife Refuge 
CVPIA – Annual Report for Fiscal Year 2004 10 

areas. A base level of supply (referred to as Level 2 supplies) was made available immediately; 

the remaining portions of their full supply (referred to as Level 4 supplies) were to be made 

available in 10 percent increments over 10 years. The total amount of water to be supplied 

annually to the 14 refuge units is approximately 560,000 acre-feet (af), with limited reductions 

under certain hydrologic circumstances. CVPIA’s increased refuge water supplies will enable 

managers to enhance existing habitats, expand their wetland base, and provide increased 

benefits to a greater number of wetland-dependent species. 

The amounts of water to be supplied and the schedule for delivery were prescribed in the Act. 

In several instances, however, facilities to convey the requisite water supplies to the various 

wetland units were not in place. Consequently, the primary focus in the Refuge Water Supply 

Program has been to develop the necessary conveyance capacity, independently or through 

agreements with other parties, and to acquire the water to meet the prescribed needs. 

In addition, a program was implemented to provide 

incentives to farmers to keep agricultural fields 

flooded during the winter months to provide greater 

amounts of habitat and increased food availability. 

Dubbed the Agricultural Waterfowl Incentives 

Program, it provided tremendous benefits at 

relatively low costs per acre by providing 

supplemental habitat and an expanded food base, 

helping to reduce disease by spreading birds out 

over a wider area. The primary focus was on fields 

with waste grain crops, primarily in the Sacramento 

Valley. Unfortunately, this program, with its 

conjunctive use of lands for agriculture and 

waterfowl, has expired. 

The Focus and Priorities for Other Fish and Wildlife and Associated Habitats. The 

CVPIA directs us to make all reasonable efforts to address the environmental impacts of the 

CVP that are not specifically dealt with in the other provisions of the Act. However, identifying 

the impacts of the CVP some 50 years after it was initiated is problematic at best, especially for 

those indirect effects that were realized in the CVP 

service area. Our approach has been to initiate a 

habitat trends analysis to be used as one of several 

tools to determine what habitats, and consequently 

what species, experienced the greatest reductions 

over the last half-century in areas affected by CVP 

operations or water service. In the interim, while the 

data are gathered and analyzed, the focus of our 

efforts has been on habitat protection and restoration 

for those species in the CVP operations and service 

area that are in greatest need of assistance, primarily 

listed threatened and endangered species not 

addressed in other provisions of the CVPIA, some of 

which are on the verge of extinction. Emphasis has 
CVPIA – Annual Report for Fiscal Year 2004 11 

been on habitat acquisition for protection and restoration of species such as the riparian brush 

rabbit, giant garter snake, vernal pool invertebrates, and San Joaquin Valley floor species like 

the San Joaquin kit fox, blunt-nosed leopard lizard, and several listed species of kangaroo rats. 

Concurrently, the CVPIA Land Retirement Program is acquiring land which, when retired from 

irrigated agriculture and restored or allowed to revert to natural conditions, will provide 

habitat for many of these same species. 

Coordination

Cooperation through partnerships with others is essential to the CVPIA’s success. We have 

developed many partnerships and extensive coordination linkages with local, State, and Federal 

agencies and private groups. These partnerships are with many previously existing programs 

as well as with programs and groups formed specifically to carry out CVPIA mandates. CVPIA 

implementation is closely coordinated with existing and ongoing restoration efforts such as the 

State of California’s efforts to restore salmon and steelhead populations, the State Water 

Resources Control Board’s (SWRCB) Water Quality Control Plan for the Delta, and the CALFED 

Ecosystem Restoration Program (ERP). In addition, most CVPIA restoration actions are 

developed and/or implemented in conjunction with local interest groups, many formed 

specifically for the purpose. 

Coordination with the ERP is particularly important. Many of their actions have the same or 

similar objectives, and address the same natural resource and water management problems as 

the CVPIA. Close coordination and a focus on functional integration of both programs have 

helped us to achieve common goals and to avoid duplication. An example of this coordination 

is Interior’s willingness and effort to have ERP scientists provide “expert level” review and 

comment on proposed CVPIA programs and actions. This review is expected to lead to a more 

broad-based ecosystem management strategy that more effectively addresses fish and wildlife 

mitigation, restoration, and enhancement, and assists in the selection of worthy projects 

We have also encouraged the ERP and other potential partners to enter into cooperative 

relationships to implement appropriate CVPIA measures or to help achieve CVPIA goals and 

objectives through their own programs. Frequently, Interior will provide funds and services to 

these partners for them to undertake pre-approved restoration actions that help to attain CVPIA 

goals. At other times, funds from these other programs or partners are used to implement 

measures identified by CVPIA. Regardless of who implements which measures, Interior first 

assures that CVPIA funds are used only to meet CVPIA goals and objectives. Additionally, 

implementation of the CVPIA has routinely involved the CVP water and power users and other 

interested parties, including the discussion of priorities and efficient use of funds. 

Funding Sources

Implementation of the prescribed actions and programs of the CVPIA through the first 12 years 

(1993 – 2004) has cost approximately $759.4 million. Many of the measures implemented 

pursuant to CVPIA were already being planned or in progress at the time the Act was passed 

and a large portion of these expenditures would have occurred even in the absence of the 

CVPIA. These include the Shasta Temperature Control Device ($84 million to implement but 

saving $5 million per year in lost power generation), Glenn-Colusa Irrigation District Fish 

Screen Project (cost - $41 million), rehabilitation of Coleman National Fish Hatchery (cost - $21 
CVPIA – Annual Report for Fiscal Year 2004 12 

million), and fixing the fish passage problems at the Red Bluff Diversion Dam (RBDD) (cost - 

$42 million) and at the Tracy and Contra Costa Canal Pumping plants (cost - $22 million). 

Other efforts, however, such as the Anadromous Fish Restoration Program (AFRP), Clear Creek 

Restoration Program, Spawning Gravel Replenishment Program, Anadromous Fish Screen 

Program (AFSP), Refuge Water Supply Program, and the Comprehensive Assessment and 

Monitoring Program (CAMP) became realities only because of CVPIA-provided funding. 

Most of the $759.4 million spent thus far has come from the Restoration Fund that was 

established in accordance with CVPIA Section 3407. These funds are derived from fees paid by 

the beneficiaries of the CVP’s water and power supplies. The rest of the monies came from 

Reclamation’s Water and Related Resources appropriations, from contributions provided by the 

State of California, and from donated funds. 

For FY 2004, more than $66.5 million was allocated by Interior for the various CVPIA programs 

and actions. Nearly 60 percent of this allocation was provided from the CVPIA Restoration 

Fund. 

Since its inception more than seven years ago, the ERP facilitated funding for a variety of 

projects contributing to ecosystem restoration within its geographic scope. The ERP is designed 

to maintain, improve, and increase aquatic and terrestrial habitats and improve ecological 

functions in the San Francisco Bay and Sacramento-San Joaquin Delta (Bay-Delta) to support 

sustainable populations of diverse and valuable plant and animal species. Most of the ERP’s 

goals and geographic scope overlap with CVPIA goals. Thus, CALFED agencies have 

established a “Single Blueprint” for restoration and species recovery within the geographic 

scope of the ERP. 

The Single Blueprint requires CALFED to integrate with numerous programs. With respect to 

CVPIA, there is much coordination between the Anadromous Fish Restoration Program, 

Anadromous Fish Screen Program, Dedicated CVP Water for Environmental Purposes, Clear 

Creek Program, Gravel Replenishment Program, and to a lesser extent, the Habitat Restoration 

Program. The Single Blueprint approach helps ensure coordination and integration, not only 

within the Bay-Delta Program, but between all resource management, conservation, and 

regulatory activities affecting the Bay-Delta system. As a result, many CVPIA projects receive 

leverage funding from the ERP program. 

Figures 1 and 2 on page 13 show the obligations by fund source, Figure 1 for the 12-year period 

since FY 1993 and Figure 2 for FY 2004 alone. The largest portion of the monies obligated since 

1993 have been spent on anadromous fish restoration-related structural measures, such as the 

Shasta Temperature Control Device and the Glenn-Colusa Irrigation District Fish Screen Project. 

These projects benefit the water and power users as well as anadromous fish. Large amounts 

were also obligated on habitat restoration measures for anadromous fish, measures believed 

necessary to help achieve our goal of doubling the natural production of these species, and on 

acquiring and providing water for refuges. On page 14, Figures 3 and 4, respectively, show the 

total distribution of these obligations among action categories for the entire FY 1993-2004 period 

and for FY 2004 alone. 
CVPIA – Annual Report for Fiscal Year 2004 13 

FIGURE 1

CVPIA OBLIGATIONS BY FUND SOURCE

Fiscal Years 1993-2004

57%

34%

4%

5% 0%

Total-Restoration Fund $431 million

Total-Water & Related Resources

Funds $259.4 million

Total-State Past Cost Share $27 million

Total-State Current Cost Share $41

million

Total-Donated Funds $1 million

FIGURE 2

CVPIA OBLIGATIONS BY FUND SOURCE

Fiscal Year 2004

60%

30%

6% 4%

Restoration Fund $40.3 million

Water & Related Resources $19.9 million

State Past Cost Share $4.0 million

State Current Cost Share $2.5 million
CVPIA – Annual Report for Fiscal Year 2004 14 

FIGURE 3

TOTAL CVPIA OBLIGATIONS BY ACTION CATEGORY 

Fiscal Years 1993-2004

5%

11%

28%

48%

3% 3% 2% Admin./Contracts/Improved Water Mgmt.

$30.0 million

Other Fish and Wildlife $66.5 million

Anad. Fish - Habitat Restoration $169.8

million

Anad. Fish - Structures $289.2 million

Refuges & Waterfowl $173.8 million

Studies/Investigations/Modeling $20.9

million

Monitoring $9.2 million

FIGURE 4

CVPIA OBLIGATIONS BY ACTION CATEGORY

Fiscal Year 2004

37%

20%

1%

32%

0%

10%

Anad. Fish - Habitat Restoration $24.5

million

Anad. Fish - Structures $13.4 million

Studies/Investigations/Modeling $0.75

million

Refuges & Waterfowl $21.2 million million

Monitoring $0.22 million

Other Fish and Wildlife $6.7 million
CVPIA – Annual Report for Fiscal Year 2004 15 

FISCAL YEAR 2004 ACCOMPLISHMENTS AND RESTORATION FUND 

DOLLARS OBLIGATED 

Since its passage in 1992, Reclamation and the Service, with assistance of the State of California 

and the cooperation of many partners, have completed many of the CVPIA’s provisions. These 

include many of the administrative requirements, water management and operational changes, 

and contracting and water conservation measures. Many studies and investigations have been 

undertaken and completed and hundreds of measures to benefit fish and wildlife resources and 

improve water project operations have been implemented. The following provides a brief 

discussion of the status of CVPIA programs and a general overview of our activities and 

accomplishments specifically in FY 2004.

Project Title: Anadromous Fish Restoration Program

 CVPIA Section 3406(b)(1) 

FY 2004 Funding: $2,640,724 

FY 2004 Accomplishments: 

The CVPIA directed implementation of a program that makes all reasonable efforts to ensure 

that the average natural production of six species of anadromous fish in Central Valley rivers 

and streams will be sustainable, on a long term basis, at levels at least double that existing 

during the 1967-1991 period. Anadromous fish are those species that are born in freshwater but 

migrate to saline waters as juveniles, where they spend a large portion of their lives before 

returning to freshwater as adults to spawn. The six species targeted by the CVPIA are Chinook 

salmon (four distinct races), steelhead, striped bass, American shad, white sturgeon, and green 

sturgeon. With the goal of developing and implementing this provision, Interior established the 

AFRP. 

All actions to achieve sustainable doubling of the natural production (doubling goal) of these 

species of anadromous fish were guided by the Final Restoration Plan (Plan) for the AFRP 

(Service, 2001) developed by AFRP staff in coordination with experts from many agencies and 

stakeholder groups. This Restoration Plan, finalized in 2001 after extensive input and public 

review, identified 6 general objectives necessary to achieve the doubling goal: 

1. Improve habitat for all life stages of anadromous fish through provision of flows of 

suitable quality, quantity, and timing, and improved physical habitat; 

2. Improve survival rates by reducing or eliminating entrainment of juveniles at 

diversions; 

3. Improve the opportunity for adult fish to reach their spawning habitats in a timely 

manner; 

4. Collect fish population, health, and habitat data to facilitate evaluation of restoration 

actions; 

5. Integrate habitat restoration efforts with harvest and hatchery management; and 

6. Involve partners in the implementation and evaluation of restoration actions. 
CVPIA – Annual Report for Fiscal Year 2004 16 

The Plan identified the measures believed necessary to achieve the doubling goal for each 

significant stream in the Central Valley. Reported here are the actions to achieve that goal that 

were implemented and/or funded specifically under the AFRP. Other actions to improve 

conditions for these species of anadromous fish were funded and carried out under other 

provisions of the CVPIA. Twenty of the other 22 provisions in Section 3406(b) were intended to 

contribute to that effort. Actions under these other provisions, although guided by the Plan, are 

being carried out independently and reported separately. 

 

Hundreds of AFRP restoration actions and evaluations were implemented since the passage of 

CVPIA to help achieve the CVPIA doubling goal for anadromous fish. All were extensively 

coordinated with local stakeholders in the various geographic areas and watersheds in which 

anadromous fish occur. In many cases, where local watershed groups did not previously exist, 

the AFRP worked to create them. All AFRP actions were coordinated with other agencies and 

other programs to avoid duplication and to make the most effective use of limited CVPIA 

funds. Of particular note was coordination with the ERP. The ERP has many of the same 

objectives as the AFRP. To enhance this coordination, proposed AFRP actions in recent years 

were submitted to the ERP review panels for their opinion on the priority and relative merit of 

the proposed action. Frequently, CVPIA and the ERP partnered in the implementation of 

measures. Other actions may be funded entirely by the ERP or CVPIA, regardless of which 

entity actually developed or solicited the proposal. 

The AFRP restoration objective gap analysis for each of the Central Valley watersheds was 

presented in the FY 2003 and FY 2004 workplans. Although the AFRP identified approximately 

$15.8 million in restoration projects for immediate development, sufficient funds were 

unavailable for this level of implementation. During FY 2004, the AFRP was limited to funding 

only ongoing projects (no new projects) due to a reduced budget. 

FY 2004 AFRP funded actions and accomplishments, include the following: 

Upper mainstem Sacramento River and upper Sacramento River tributaries 

Ongoing project accomplishments

1. Mainstem Sacramento River watershed: (a) continued development of an 

environmental compliance and hydraulic evaluation of the La Barranca project (Phase 

II); and, (b) completed markers to identify winter-run Chinook salmon (part of effort to 

determine the genetic impacts of the winter-run Chinook salmon captive broodstock 

program on the wild winter-run Chinook salmon population through genetic analysis).

2. Continued assistance to the Cow Creek watershed management group in their 

watershed management plan proposal preparation. Completion of this plan will have 

incorporated all AFRP Restoration Plan actions and evaluations for Cow Creek that 

address limiting environmental factors to doubling anadromous fish populations in this 

stream. 

3. On Cottonwood and Deer Creek watersheds, Habitat Restoration Coordinators (HRC) 

continued to provide coordination, technical guidance, and proposal development of the 
CVPIA – Annual Report for Fiscal Year 2004 17 

CALFED Environmental Water Program (EWP) on Deer and Clear creeks, two of the 

five EWP priority streams. 

4. Lower Butte Creek watershed: (a) continued funding Ducks Unlimited as the project 

manager of the Lower Butte Creek Project (LBCP), which has the objective of modifying 

five flow control structures and fish ladders to improve fish passage; (b) completed 

engineering designs and necessary environmental documentation on all five reaches of 

the LBCP; (c) completed Phase II on the Butte Sink and Sutter Bypass West Side reaches 

and nearing completion on the White Mallard and Associated Diversions reach of the 

LBCP; (d) developed a Memorandum of Understanding (MOU) between stakeholders 

and agency representatives to address the large number of small pumps and multitude 

of diversions and weirs located on Butte Slough and Sutter Bypass East; (e) constructed 

three weirs located on the west side of the Sutter Bypass; (f) constructed five water 

control structures in the Butte Sink; (g) initiated construction of two adult fish barriers; 

and, (h) negotiated purchase of a long-term water right for in-stream flows in the west 

side Sutter Bypass. 

5. On the Feather River watershed, the Program evaluated limiting factors for sturgeon 

and salmon passage and spawning which is continuing through the FERC settlement 

process for Oroville Dam relicensing. 

FY 2004 funded ongoing projects

1. On Butte and Big Chico creeks the Program provided additional funding for continued 

implementation of a 10-year salmonid life history study that evaluated the effectiveness 

of restoration projects relative to abundance, habitat use, growth, survival, fish passage, 

and many other factors. Some of the interim study findings include: (a) juvenile 

residency time in Butte Creek ranged from 56 days to 71 days in 1998 through 2000; (b) 

adult spring-run Chinook salmon (SRCS) escapement during 1999 and 2000 were 3,679 

and 4,119 fish respectively, exceeding the 2000 fish doubling goal both years; and (c) 

ocean tag recoveries from Butte Creek adults captured in the commercial/sport fishery 

suggest that some portion of Butte Creek SRCS return to spawn as age four fish. 

Another particularly important study element will evaluate growth of juvenile salmon 

that rear and migrate through the Sutter Bypass compared to those that use the 

mainstem Sacramento River. These interim data serve as a basis for new restoration 

projects as well as provide a baseline for post-project evaluation of effectiveness. In 

addition, these data are being incorporated into the National Oceanic and Atmospheric 

Administration (NOAA) Fisheries spring-run Chinook salmon recovery effort, the 

fishery management plan conservation objectives for the Pacific Fishery Management 

Council, and the Interagency Ecological Program Sacramento River Delta Operations 

Plan. 

2. Continued to assist locally led efforts to facilitate coordination of the Butte Sink/Sutter 

Bypass stakeholders as identified in #4 above. Other Project activities include Project 

tours, outreach and education and attendance of CBDA/ERP associated meetings. 
CVPIA – Annual Report for Fiscal Year 2004 18 

3. Funded the permitting phase of the Drumheller Slough 5-points Screen Project. This 

project looks at the final alternative for the West of Butte Creek Drumheller Slough-5 

points fish screen and alternative routing of the RD 1004 diversion from Butte Creek. 

The final plan will amend the existing Negative Declaration/FONSI and Biological 

Assessment. 

Lower Sacramento River and Delta tributaries 

Ongoing project accomplishments

1. Yuba River watershed: (a) replaced the existing temporary outlet barrier with a 

permanent "leaky-dike" barrier to prevent the migration of Yuba River Chinook salmon 

and steelhead into the Goldfields, which is an active dredger mining operation; (b) 

completed year one of tagging for juvenile life history study; (c) completed year one 

sampling for the Spawning Habitat Integrated Rehabilitation Approach which balances 

fish habitat needs with fluvial geomorphic process goals; and (d) continued negotiations 

with key lower Yuba River Stakeholders involved in the State Water Resources Control 

Board Revised Decision 1644. 

2. American River Watershed: Initiated research to develop predictive tools that will: (a) 

reduce, to the extent possible, the uncertainties in the performance of identified 

temperature control actions that could be implemented to improve the management of 

cold water resources in the Folsom/Natoma Reservoir system and the lower American 

River, and (b) be available for daily operations, planning, and salmon and steelhead 

habitat studies by other project operators and other stakeholders. Completed first year 

of a two year project (completion date is September 26, 2005) sampling and modeling of 

the Lower American River temperature reduction modeling project. 

3. Bear River watershed: (a) identified fish passage impediments on Dry Creek, tributary 

to Bear River; and (b) developed a baseline conditions study for the lower Bear River. 

4. Calaveras River watershed: (a) completed fall-winter 2003-04 adult and juvenile 

Chinook salmon surveys downstream of Bellota Weir; (b) retrofitted Bellota Weir Fish 

ladder; and, (c) completed first year report of the Lower Calaveras River salmonid lifehistory study. 

5. Cosumnes River watershed: (a) assessed flow requirements for upstream passage of 

adult fall-run Chinook salmon; (b) estimated flow augmentation needs and water 

sources to allow upstream salmon passage in the fall; and, (c) continued salmon barrier 

improvement work. 

6. Mokelumne River watershed: (a) added 1,200 cubic yards of gravel in bar 

configurations perpendicular to flow as part of the first year of the Mokelumne River 

Spawning Habitat Improvement Project; (b) completed analysis of sediments above and 

below Murphy Creek to assess post-dam processes and changes, providing a baseline to 

minimize disturbances in downstream rearing areas; and, (c) completed two peer 
CVPIA – Annual Report for Fiscal Year 2004 19 

reviewed UC Davis publications resulting from the interdisciplinary project approach to 

rehabilitate salmonid spawning habitat. 

FY 2004 funded ongoing projects 

1. In relation to the Mokelumne River Spawning Habitat Improvement Project, additional 

dollars were used to purchase gravel in 2004 and complete this two year project. Similar 

past investments in spawning habitat improvement have resulted in immediate 

increased utilization by Chinook salmon spawners. Similar results are anticipated with 

partnered investment with East Bay Municipal Utility District. 

2. An interdisciplinary approach to gravel augmentation was implemented on the 

Mokelumne River. Funds were provided to manage a large volume of field data, 

coordinate it with other databases and transform it into easily understandable 

management information suitable for a variety of stakeholders. This funding will also 

allow modeling gravel movement at a wider range of flows to better estimate future 

gravel augmentation rates. 

San Joaquin Basin tributaries and mainstem San Joaquin River 

Ongoing project accomplishments

1. Stanislaus River watershed: (a) continued field testing and design modification of the 

Vaki infrared fish counter during the fall-run escapement from September 2003 through 

April 2004; (b) completed 50 percent of a draft plan to restore anadromous fish habitat in 

the Stanislaus River (http://www.delta.dfg.ca.gov/srfg/); (c) completed an annual 

rotary screw trap monitoring efforts at Caswell State Park; (d) progressing on 

environmental permitting for spawning and rearing, floodplain and side channel habitat 

restoration in the Lover’s Leap and Knights Ferry reaches; (e) continued to plan and 

coordinate with USBR for spawning gravel introduction below Goodwin Dam; and, (f) 

completed riparian revegetation and floodplain restoration on the Mohler Tract. 

2. Tuolumne River watershed: (a) continued channel and floodplain restoration at the 

7/11 materials restoration site; (b) reviewed preliminary appraisals for the MJ Ruddy 

restoration project by Interior (restoration and construction is anticipated to start in July 

of 2005); (c) completed preliminary design engineering and environmental permitting on 

the Warner-Deardorff channel and floodplain restoration site in preparation for the 

CBDA funded and AFRP managed Warner-Deardorff restoration project; (d) initiated 

the environmental permitting, design engineering and pre-project monitoring at the 

Tuolumne Special Run Pool 10 site; (e) continued third-year post-project monitoring of 

the Grayson River Ranch floodplain restoration project (conservation easement) on the 

Tuolumne River; (f) developed an interpretive and education facility concept on the 

upper Tuolumne River with Stanislaus County; (g) amended Sediment Management 

Plan agreement to incorporate short term habitat needs and adaptive management 

methods to guide future gravel augmentation management practices; and (h) completed 

the Tuolumne River Technical Advisory Committee’s scope of work for the Tuolumne 

River gravel transfusion project to include additional gravel supply methods. 
CVPIA – Annual Report for Fiscal Year 2004 20 

3. Merced River watershed: (a) completed preliminary results of hydraulic modeling of 

fish habitat benefits of post-restoration at the Robinson Ranch Reach (the AFRP hired the 

USFWS Energy and In-stream Flow Branch to conduct Physical Habitat Simulation 

studies of the area); (b) completed preliminary design engineering and landowner 

coordination at the lower Western Stones restoration site; (c) completed all three 

Adaptive Management Forum (AMF) reports (Tuolumne, Merced, and Clear Creek 

reports are available on the AFRP web site); (d) completed water temperature data 

assessment by Merced Irrigation (available on the AFRP web site); (e) purchased 20 

water quality test kits to encourage landowner water testing in coordination with the 

East Merced Resource Conservation District; (f) initiated negotiations with the local 

mining industry concerning reclamation plans for Bettencourt Ranch mining project; 

and, (g) continued support of the Merced River Dredger Tailings Reach phase I adaptive 

management studies and restoration. 

4. On the mainstem San Joaquin River, the San Joaquin River National Wildlife Refuge 

wetlands plans were incorporated into hydraulic modeling efforts funded by AFRP to 

evaluate proposed non-structural flood control management alternatives on the Refuge. 

5. San Joaquin Basin: (a) completed 75 percent of a California Department of Fish and 

Game (CDFG) riffle atlas study to provide a comprehensive San Joaquin Basin riffle 

inventory; (b) completed draft feasibility study report for developing a long-term 

aggregate source for San Joaquin tributary channel restoration projects; (c) completed 80 

percent of a CDFG study to read archived Chinook salmon scale samples from the San 

Joaquin Basin to be used to update a salmon population model that assists alternative 

flow management evaluations on the tributaries. 

6. Comprehensive program accomplishments included: (a) renovation of existing website 

to provide more user-friendly access to information; and, (b) updating and expanding 

scope of information available on the web site. 

FY 2004 funded ongoing projects

1. The Two Mile Bar spawning habitat/floodplain restoration project (Phase 1) will restore 

the floodplain and sediment processes in a critical spawning and rearing reach of the 

Stanislaus River. Environmental permitting is underway to include floodplain and sidechannel restoration. The California Department of Water Resources (CDWR) has 

contributed $500,000 to the project through the Four Pumps Mitigation effort. 

2. Chinook salmon and steelhead life history evaluation was continued to include 2004 

analysis and reporting of fish passage data (e.g., VAKI). 

3. In an effort to develop data needs, AFRP funded: (a) data development for a sediment 

study on Murphy Creek, a tributary to the Mokelumne River; (b) Merced River 

stakeholder group facilitation; (c) a mineral appraisal for MJ Ruddy project on the 

Tuolumne River, (d) project proposal preparations; and, (e) an adjustment to a 

Tuolumne River sediment management plan to include steelhead. 
CVPIA – Annual Report for Fiscal Year 2004 21 

Project Title: Evaluation of Anadromous Fish Instream Flow Needs

 CVPIA Section 3406(b)(1)(B) 

FY 2004 Funding: $480,165 (provided by AFRP) 

FY 2004 Accomplishments: 

In directing Interior to make all reasonable efforts to at least double the natural production of 

anadromous fish, Congress recognized the need for flows of suitable quality, quantity, and 

timing in those streams that support these species. It specifically directed that the instream flow 

necessary to protect all life stages of anadromous fish on CVP-controlled streams be determined 

by the Service after consultation with CDFG. However, to achieve the goal of doubling the 

natural production of anadromous fish throughout the Central Valley, the flow needs of these 

species on other Central Valley streams and rivers must also be ascertained so that actions may 

be taken to provide for those needs. Instream flow studies had already been conducted on 

several streams. With the passage of the CVPIA, those previous evaluations are being reviewed 

and additional studies conducted. These efforts have been under way for several years and will 

continue for several more. 

FY 2004 accomplishments were documented in the annual status report entitled “Identification 

of the Instream Flow Requirements for Anadromous Fish in the Streams within the Central 

Valley of California” for the following seven tasks. Task 1 addressed steelhead spawning and 

Chinook salmon and steelhead rearing in the Yuba River; Tasks 3 and 4 addressed Chinook 

salmon and steelhead rearing in the Yuba River, and Chinook salmon and steelhead spawning 

in Clear Creek; and Tasks 5 and 6 addressed Chinook salmon spawning in the Sacramento 

River between Battle Creek and Deer Creek, and juvenile Chinook salmon rearing in the 

Sacramento River between Keswick Dam and Battle Creek. 

1. Habitat Suitability Criteria (HSC) Development - Completed collection of spawning 

HSC data for fall- and spring-run Chinook salmon and steelhead/rainbow trout in the 

Yuba River in FY 2004. We continued collecting rearing HSC data for fry and juvenile 

fall/spring run Chinook salmon and steelhead/rainbow trout in FY 2004. Spawning 

HSC data collection is 100 percent complete and rearing HSC data collection is 60 

percent complete. 

2. Habitat Mapping - There were no activities for this task in FY 2004. Habitat mapping for 

the Yuba River was completed in FY 2003, and habitat mapping for Clear Creek will be 

conducted in FY 2005. 

3. Field Reconnaissance and Study Site Selection - Established eight study sites for 

Chinook salmon and steelhead/rainbow trout fry and juvenile rearing in the Yuba 

River, and established five study sites for Chinook salmon and steelhead/rainbow trout 

spawning in Clear Creek. The above activities are 100 percent complete. 

4. Hydraulic Data Collection - Continued hydraulic data collection for Chinook salmon 

and steelhead/rainbow trout spawning sites on the Yuba River and started hydraulic 

data collection for Chinook salmon and steelhead/rainbow trout fry and juvenile 

rearing sites on the Yuba River and Chinook salmon and steelhead/rainbow trout 

spawning sites on Clear Creek. All of the above hydraulic data collection should be 
CVPIA – Annual Report for Fiscal Year 2004 22 

completed in FY 2005. Hydraulic data collection is 95 percent complete for Yuba River 

spawning, 80 percent complete for Yuba River rearing, and 90 percent complete for 

Clear Creek spawning. 

5. Modeling of Spawning and Rearing Habitat in Study Streams - Modeling of fall-run 

Chinook salmon spawning habitat in the Sacramento River between Battle and Deer 

Creeks began in FY 2004. Modeling of rearing habitat in the Sacramento River between 

Keswick Dam and Battle Creek was nearly completed (greater than 95 percent) in FY 

2004, and will be 100 percent completed in early FY 2005. 

6. Peer Review - There was no activity for this task in FY 2004. The report for rearing 

habitat in the Sacramento River between Keswick Dam and Battle Creek will be peer 

reviewed in FY 2005. 

7. Program Management - Project coordination meetings were held and a project progress 

report was prepared in FY 2004. This activity is 50 percent complete. 

Project Title: Habitat Restoration Program

 CVPIA Section 3406(b)(1) “Other” 

FY 2004 Funding: $1,430,614 

FY 2004 Accomplishments: 

The Habitat Restoration Program (HRP) was established to protect and restore habitats 

impacted by the CVP that were not specifically addressed elsewhere in the CVPIA and to 

stabilize and improve populations of native species that relied on those habitats. The program’s 

initial focus was on those habitats known to have experienced the greatest decline in habitat 

quantity and quality and on species that were listed, proposed, or candidates for listing under 

the ESA or were non-listed State or Federal species of special concern. 

The program began in FY 1996 and has funded 69 projects located throughout the Central 

Valley at a cost of approximately $21.2 million. Approximately 98,179 acres of habitat for listed, 

proposed, and candidate species and species of special concern have been protected, often 

through partnerships with others in fee title acquisitions or conservation easements. Habitats 

protected include vernal pool, aquatic, alkali scrub, foothill chaparral, valley-foothill hardwood, 

and grassland. 

In FY 2004, eight conservation actions were funded. Two of these actions provided additional 

funding to continue projects that were initiated in previous years. These are continued 

monitoring for giant garter snakes at the habitat restoration site that the program funded at the 

Colusa National Wildlife Refuge and trapping and surveying for giant garter snakes at the San 

Luis National Wildlife Refuge. 

The six actions that were new to the program and funded in FY 2004 include the following: 

1. Funds were provided for the Adaptive Vegetation Management on Serpentine Soils 

Study, to assess grazing impacts on native serpentine plant species on Coyote Ridge in 
CVPIA – Annual Report for Fiscal Year 2004 23 

Santa Clara County. Developing this information and applying it in adaptive land 

management are priority tasks for recovery of the bay checkerspot butterfly, Santa Clara 

Valley dudleya, Metcalf Canyon jewelflower, and other species. 

2. Funds were provided to the Nature Conservancy for riparian restoration on 206 acres on 

the Ohm property along the Sacramento River in Tehama County. Species that would 

benefit include the valley elderberry longhorn beetle and bald eagle. 

3. Funds were provided to River Partners for the Drumheller Slough Riparian Restoration 

project. Riparian restoration would occur on 226 acres on Drumheller Slough within the 

Sacramento River National Wildlife Refuge in Glenn County. The valley elderberry 

longhorn beetle and giant garter snake would benefit. 

4. Funds were provided to the Bureau of Land Management for fee title acquisition of 

5,810 acres of the Ansin property, located inside and outside of the Carizzo Plain 

National Monument in Kern County. Habitat is comprised of alkali scrub, saltbush 

scrub, and semi-desert scrub. Species that would benefit include the San Joaquin kit fox, 

blunt-nosed leopard lizard, giant kangaroo rat, San Joaquin wooly threads, and Kern 

primrose sphinx moth. 

5. Funds were provided to the Trust for Public Lands for fee title acquisition of 708 acres of 

oak woodland and riparian habitat at the mouth of Fine Gold Creek, tributary to the San 

Joaquin River in Madera County. Species that would benefit include the valley 

elderberry longhorn beetle, bald eagle, and California tiger salamander. 

6. Funds were provided to the Central Valley Habitat Joint Venture for buy-in to a habitat 

restoration “clearinghouse” webpage and to gain access to valley-wide project data. 

Project Title: San Joaquin River Riparian Habitat Restoration Program

 CVPIA Section 3406(b)(1) “Other” 

FY 2004 Funding: $715,732 

FY 2004 Accomplishments: 

The San Joaquin River Riparian Habitat Restoration Program (SJRRHRP) is a consensus-based 

group of Federal, local, and non-governmental organizations that have an interest in restoring 

riparian habitat on the San Joaquin River. The SJRRHRP was formed in 1997 at the request of 

the non-Federal litigants engaged in discussions about mutually acceptable restoration activities 

on the San Joaquin River in conjunction with the Natural Resources Defense Council (NRDC) v. 

Rodgers lawsuit. Reclamation and the Service, the Friant Water Users Authority (FWUA), 

NRDC, and Pacific Coast Federation of Fishermen’s Associations were the original parties. In 

subsequent years, the San Joaquin River Exchange Contractors Water Authority also became 

involved. The SJRRHRP provides funding for proposed and on-going efforts to gather data 

and/or disseminate information that will support the restoration of riparian habitat and 

functions along the San Joaquin River. 
CVPIA – Annual Report for Fiscal Year 2004 24 

When the FWUA and NRDC were actively conducting their San Joaquin River restoration and 

water supply investigations, the SJRRHRP provided assistance on the experimental programs 

and activities that supported the data gathering necessary for their NRDC v. Rodgers settlement 

discussions. With the FWUA and NRDC settlement discussions now terminated, FY05 

activities would most likely provide support for Reclamation, Service and CDWR San Joaquin 

River related planning activities. 

FY 2004 actions funded and accomplishments include the following: 

1. CDFG initiated a 4-year Milburn-Hansen Restoration Planning Project. CDFG, in 

coordination with CDWR, will be conducting the planning, pre-design, biological 

surveys, engineering, re-vegetation planning, environmental analysis, and public 

outreach activities necessary to outline a restoration plan for the abandoned aggregate 

mining pit areas in the Milburn Unit and the state-owned lands adjacent to Hansen 

Farm property. 

2. CDFG initiated a 2-year Fishery and Aquatic Resources Inventory. CDFG will inventory 

and document the present-day status, distribution, and condition of aquatic fauna and 

flora between Friant Dam and the confluence of the Merced River. The documentation 

will include water condition information pertinent to interpretation of the inventory 

results. 

3. Point Reyes Bird Observatory (PRBO) continued their 3-year monitoring program that is 

a collection of baseline data. Annually from 2003 through 2006, PRBO will provide 

baseline information on riparian bird communities including presence-absence, habitat 

associations, density (birds per acre), and some demographic indices (fidelity, 

productivity, and survivorship) to measure population health along the mainstem of the 

San Joaquin River from Friant Dam to the confluence of the Merced River. This effort 

builds upon the bird monitoring activities PRBO conducted for SJRRHRP in 2002. 

4. U.S. Department of Energy, Lawrence Berkeley National Laboratories (LBNL) designed 

and installed additional water quality monitoring systems at various points along the 

San Joaquin River. LBNL will also make recommendations on a water quality 

monitoring and decision support system for the San Joaquin River between Friant Dam 

and the confluence of the Merced River. Monitoring equipment installation is to be 

completed by December 2004. 

5. California State University B Stanislaus Foundation, Endangered Species Recovery 

Program (ESRP) continued gathering the terrestrial biological surveys and related 

studies that were initiated in 2000. ESRP is conducting surveys for valley elderberry 

longhorn beetles (and their habitat), small mammals (especially kangaroo rats), canids 

(especially San Joaquin kit foxes), and other species upon request. 

6. Funds were provided to obtain a variety of clean up materials and to cover the trash and 

tire disposal fees for a San Joaquin River cleanup efforts led by the City of Firebaugh in 

recognition of the April 2004 “Keep California Beautiful” campaign and a clean up led 
CVPIA – Annual Report for Fiscal Year 2004 25 

by RiverTree Volunteers in recognition of the May 2004 “National River Clean Up 

Week”, the September 2004 “California Coastal Commission’s Clean Up Day” and the 

federal “National Public Lands Day.” 

7. National Park Service, in cooperation with the National Film Arts Foundation, 

completed an oral history film documentary “Jewel of the San Joaquin – Andrew 

Firebaugh Historical Park, Firebaugh, California.” It portrays the City of Firebaugh’s 

role and significance to the San Joaquin River. 

8. The review and completion of the Biological Assessment and Section 7 consultation with 

the Service on the Jensen River Ranch restoration planning effort was completed. 

9. Information was obtained that identified what would be required, on a demonstration 

level, to reduce the amount of aquatic invasive species (e.g. Parrot’s Feather) in the San 

Joaquin River downstream of Friant Dam. 

10. An inventory and compilation of all Riparian Program-funded documents prepared by 

contractors and Reclamation staff was completed. 

Project Title: Management of Dedicated CVP Water for Environmental 

Purposes

 CVPIA Section 3406(b)(2) 

FY 2004 Funding: $704,565

FY 2004 Accomplishments: 

On October 6, 1999, Interior released its “Final Decision on Implementation of Section 3406 

(b)(2).” That decision, and its accompanying attachments, provided a calculation of CVP water, 

identified the method of accounting for use of the dedicated CVP water pursuant to CVPIA, set 

out procedures for management of the water, and listed potential measures which may be 

prescribed by the Service for use of the dedicated water. However, a decision by the Federal 

District Court in March 2002 ruled that portions of Interior’s accounting methodology were 

erroneous. Consequently, Interior revised its procedures for accounting and managing the 

dedicated CVP water to comport with the Courts’ rulings and, in May 2003, issued a “Final 

Decision on Implementation of Section 3406 (b)(2). This new decision was implemented 

beginning in October 2003. 

Reclamation, Service, NOAA Fisheries, CDWR and CDFG established an Environmental Water 

Account (EWA) to provide protection (supplemental to a baseline level of protection) to the fish 

of the Bay-Delta estuary. The management of the (b)(2) water is part of that baseline and is 

closely coordinated with the management of the EWA. 

In FY 2004, work continued on an updated Operations, Criteria and Plan (OCAP) and OCAP 

Biological Assessment. A non-jeopardy biological opinion for the delta smelt was issued by the 

Service on July 30, 2004. The updated OCAP includes the revised decision on implementation 

of the dedicated water, the EWA, the Freeport diversion, and the California Aqueduct-DMC 
CVPIA – Annual Report for Fiscal Year 2004 26 

intertie. This biological assessment also included as early consultation the South Delta 

Improvement Program which included the pumping of 8,500 cfs at Banks pumping plant. 

The “Final Decision on Implementation of Section 3406(b)(2)” from May 2003 was implemented 

for the first year and coordinated with the fourth year implementation of the EWA. These 

measures contributed to the CVPIA’s goal of doubling natural production of anadromous fish 

and provided concurrent benefits to other fish and wildlife, including endangered species. 

Monitoring and evaluation to assess the effectiveness of the implemented (b)(2) environmental 

measures continued. 

FY 2004 accomplishments include the following: 

1. Prepared annual operations forecast representing the 1992 baseline conditions and the 

1995 Water Quality Control Plan conditions. An annual (b)(2) fishery action plan was 

prepared based upon the operations forecast and consultation with other Federal and 

State agencies. A final operations forecast was then developed, and the forecast was 

updated on a monthly basis. 

2. Developed a preliminary accounting of (b)(2) water on the 15th day of every month, 

showing the current accounting for the accounting year as of the end of the previous 

month. Final accounting for all (b)(2) actions for the entire water year was calculated by 

October 31. 

3. Reviewed an updated Operations Criteria and Plan (OCAP) for CVP and SWP in 

support of Bay-Delta Actions. The OCAP addressed the Bay-Delta and Coordinated 

Operations Agreement (COA) obligations and reflected the AFRP, the (b)(2) and EWA 

implementation scenarios, in addition to operational modifications, such as the South 

Delta Improvement Program (8,500 cfs), Trinity Record of Decision (ROD) flows, 

DMC/CA intertie, etc. 

4. Included stakeholders and public input on the annual (b)(2) fishery action plan and how 

the plan was integrated into the operations forecast. Stakeholders as well as the public 

were included in Revised Decision and the updated OCAP. 

5. Continued monitoring and evaluation that assessed the effectiveness of (b)(2) measures. 

6. Evaluated the computer model to assess various (b)(2) implementation scenarios and 

integration of preliminary water acquisition decisions developed in FY 2001 

implementation strategy. The evaluation contributed to an integrated environmental 

water plan, including level 2 and level 4 refuge water supplies. 
CVPIA – Annual Report for Fiscal Year 2004 27 

Project Title: Water Acquisition Program

 CVPIA Section 3406(b)(3) 

FY 2004 Funding: $14,614,545 

FY 2004 Accomplishments: 

The CVPIA Water Acquisition Program is charged with the responsibility of obtaining, by 

various means, water to supplement the 800,000 af of dedicated CVP water and to assist in 

meeting the CVPIA requirements for refuge water needs (approximately 159,000 af for Level 4 

refuge water supplies). In FY 2004, the Water Acquisition Program continued efforts to: 

1. Provide supplemental water supplies for refuges, referred to as Incremental Level 4, for 

critical wetland habitat supporting resident and migratory waterfowl, threatened and 

endangered species, and wetland dependent aquatic biota. 

2. Investigate the potential of using groundwater resources, including conjunctive use, to 

augment Incremental Level 4 supplies. 

3. Acquire instream flows in support of the Vernalis Adaptive Management Plan (VAMP) 

and the San Joaquin River Agreement (SJRA). 

4. Coordinate planning efforts for instream acquisitions under CVPIA with the CALFED 

Environmental Water Program and Environmental Water Account to provide fishery 

benefits. 

Outstanding issues to address include financial constraints on the acquisition of 100 percent of 

Incremental Level 4 supplies due to the increasing price of water and inadequate funding due 

to limits of the Restoration Fund. A summary of water purchases and executed agreements for 

FY 2004 is provided in the following table: 

Delivery 

Period Seller 

Quantity 

(AF) Cost 

Cost 

per AF Purpose 

Oct 03 Merced I.D. 12,500 $806,875 $65 

Fall attraction flows and habitat 

improvement in Merced River 

and lower San Joaquin River 

(SJR) per SJRA. (FY03 Funds) 

Apr-May 04 SJR Group 

Authority 65,591 $4,384,786 N/A Spring Flows per SJRA/VAMP 

Apr-Sep 04 

SJR Group 

Authority/ 

Oakdale I.D. 

15,000 $900,000 $60 

Flow for habitat improvement 

in Stanislaus and lower San 

Joaquin Rivers (FY03 Funds) 

Jul - Sep 04 Oakdale I.D. 5,120 $307,200 $60 

Oakdale I.D. difference water 

from VAMP 2004 (per SJRA). 

(FY03 Funds) 

Jan – May 04 N/A N/A $283,000 N/A VAMP environmental 

monitoring 

Apr 04-Feb 05 Broadview 

Water District 5,400 $594,000 $110 Level 4 refuge water, contract year 2004 

Apr 04 Del Puerto 

Water District 2,100 $136,500 $65 Level 4 refuge water, contract 

year 2004 
CVPIA – Annual Report for Fiscal Year 2004 28 

Delivery 

Period Seller 

Quantity 

(AF) Cost 

Cost 

per AF Purpose 

May 04-Feb 05 

Patterson 

Irrigation 

District 

10,000 $1,000,000 $100 Level 4 refuge water, contract 

year 2004 

May – Dec 04 

San Joaquin 

River Exchange 

Contractors 

Water Authority 

47,200 $6,136,000 $130 Level 4 refuge water, contract 

year 2004 

TOTALS 162,911 $14,548,361 

- Total cost for Fiscal Year 2004 includes funds obligated in Fiscal Year 2003. 

Project Title: Tracy Pumping Plant Mitigation Program

 CVPIA Section 3406(b)(4) 

FY 2004 Funding: $3,401,423 

FY 2004 Accomplishments: 

The goal of the Tracy Pumping Plant Mitigation Program is to mitigate the impacts associated 

with the operation of the Federal Tracy Pumping Plant in the Delta. The current objectives are 

to improve fish protection and fish salvage at the facility in the short-term while determining 

the best practical fish protection technology for incorporation into long-term improvements at 

the facility. To help accomplish this, the CALFED South Delta Fish Facility forum (SDFF) has 

been meeting and establishing guidelines for how best during these times to accomplish these 

goals and objectives. 

One of the decisions the SDFF was faced with was whether or not to proceed with a test facility 

(TFTF) at Tracy. The SDFF decided to hold off on a test facility at this time until some final 

decisions could be made on what's needed to satisfy the regulatory agencies related to increased 

exports and fish protection in the south Delta. It is not anticipated at this time that a test facility 

will be constructed at Tracy, if at all, for a least a few years. 

In addition, research on fish protection technology and improvements to existing operations is 

ongoing at Reclamation’s Denver research labs, at the existing Tracy Fish Protection Facility, 

and at the University of California-Davis. 

FY 2004 accomplishments include the following: 

1. Laboratory evaluations of the TFTF fish sorting and holding physical model. 

2. Leaky louver and fish sorting studies in Denver’s large experimental flume. 

3. Studies on tracking predator fish movements inside fish salvage facilities using remote 

telemetry. 

4. Evaluation of the Tracy mitten crab traveling screen as a potential device for continuous 

woody and leafy debris removal. 
CVPIA – Annual Report for Fiscal Year 2004 29 

5. Continuation of swirl tests to assess stress levels of salvaged fish held in recessed 

collections tanks. 

6. Whole facility evaluations utilizing Delta smelt and salmon. 

7. Deployment of a technical web site. 

8. Final decision on proposed test facility. 

The research activities noted above provided valuable information towards improvements in 

fish protection at the South Delta fish facilities (both the CVP and SWP). 

Project Title: Contra Costa Canal Pumping Plant Fish Screen Project

 CVPIA Section 3406(b)(5) 

FY 2004 Funding: $39,829 

FY 2004 Accomplishments: 

This Program will provide for construction and operation of new fish screen and recovery 

facilities and for modification of operations and practices at the Contra Costa Canal Pumping 

Plant. This directive is consistent with and supports an earlier ESA Section 7 Biological Opinion 

(BO) for the delta smelt that was issued by the Service for the Los Vaqueros Project. 

In 1996, the Contra Costa Fish Screen Management Team and the Contra Costa Technical 

Advisory Committee were established, consisting of representatives from CDFG, CDWR, the 

Service, Reclamation, NOAA Fisheries, and the Contra Costa Water District. These two groups 

have been assisting in planning and developing a fish screen project for the Rock Slough intake 

of the Contra Costa Canal. In addition, there is a Peer Review Team that has helped to review 

planning and design documents and a Value Engineering Team that explored cost saving 

alternatives. 

In FY 2003, the interagency team developed an expanded fish-monitoring program, which was 

implemented in FY 2004. In addition, with the development of alternative short-term fishery 

mitigation measures, Reclamation presented these measures to the Service, NOAA Fisheries, 

and CDFG, with a request for an amendment to the Los Vaqueros BO for delta smelt. The 

amendment extended the date for completion of the Rock Slough fish screen project through 

December 2008. There is also the possibility of re-initiating formal consultation and additional 

mitigation requirements. 

Although final design and construction of a major project at the Contra Costa Canal Pumping 

Plant will await the results of the Contra Costa Water District’s studies and response from the 

fishery agencies on amendment of the BO, a short-term mitigation preliminary design was 

developed in FY 2004 and presented to regulatory agencies. 
CVPIA – Annual Report for Fiscal Year 2004 30 

Project Title: Flow Fluctuation/Reservoir Storage Management Program

 CVPIA Section 3406(b)(9) and (19) 

FY 2004 Funding: $25,722 

FY 2004 Accomplishments: 

CVPIA Section 3406(b)(9) requires development and implementation of a program to eliminate, 

to the extent possible, losses of anadromous fish due to flow fluctuations caused by operation of 

any CVP storage or re-regulating facility. This program is to be patterned, where appropriate, 

after the agreement between CDFG and CDWR, with respect to the operation of the SWP’s 

Oroville Dam complex. Closely related to this charge to reduce the impacts of flow fluctuations, 

CVPIA Section 3406(b)(19) calls for the re-evaluation of reservoir storage criteria in order to 

maintain minimum carryover storage in Shasta and Trinity Reservoirs to benefit anadromous 

fish, with full regard to the Secretary’s responsibility to fulfill all project purposes, including 

agricultural water delivery. Interior’s efforts on both of these directives are generally handled 

as a single program. However, there was no funding specifically allocated for reservoir storage 

(b)(19), under 3406(b)(2) reservoir storage was studied in FY 2004. 

The final report of the flow fluctuation study of the impacts of Folsom Dam operation on 

salmon and steelhead in the lower American River, done under contract by CDFG, was released 

in December 2001. The American River Operations Work Group met monthly throughout FY 

2004 to discuss both the American River operations and to determine threshold flows and 

ramping rates required to protect Lower American fishery resources. In addition, Reclamation 

conducted monthly temperature modeling of the flows of the American River. 

The Stanislaus River flow fluctuation study was started in 1999 and is currently ongoing. The 

early draft report of that study was released in July 2004. The Stanislaus River Operations 

Group no longer holds regularly scheduled meetings to discuss flow and temperature issues; 

however, many flow and temperature issues are discussed at the regular monthly meetings of 

the Stanislaus River Fish Group. More regular discussions of the Operations Group are held in 

the April/May period when the pulse flows for the VAMP are being planned and implemented. 

These pulse flows include releases from New Melones Reservoir on the Stanislaus River. 

Project Title: Red Bluff Diversion Dam Fish Passage Program

 CVPIA Section 3406(b)(10) 

FY 2004 Funding: $4,449,998 

FY 2004 Accomplishments: 

CVPIA Section 3406(b)(10) requires the development and implementation of measure to 

minimize fish passage problems for adult and juvenile anadromous fish at the Red Bluff 

Diversion Dam (RBDD) in a manner that provides for the use of associated CVP conveyance 

facilities for delivery of water to the Sacramento National Wildlife Refuge Complex. 

The formulation of alternatives in the first four years of the RBDD Fish Passage Planning 

Program has led to the general recognition that operations implemented as directed in the 1993 

BO for winter-run Chinook salmon are very effective in improving passage of fish with the 

possible exception of the adult spring run Chinook. The increased duration of gate removal at 
CVPIA – Annual Report for Fiscal Year 2004 31 

RBDD prompted by the BO dramatically improved baseline conditions for both juvenile and 

adult anadromous salmon and changed the standard against which additional measures to 

minimize fish passage problems would be measured. Although an estimated 80 percent of the 

adult spring run passing the RBDD are still delayed, it is unclear that this currently limits the 

recovery of this run in the upper Sacramento River and its tributaries although additional 

information may be provided as part of the OCAP BO. 

As a result, the benefits of further investments appear to be unknown pending acquisition of 

better data on the affects of dam operations on adult spring-run Chinook, but would appear to 

be low. However, State and Federal investigations of off-stream storage adjacent to the 

Tehama-Colusa Canal as part of a long-term solution to ecosystem restoration and water supply 

reliability problems could lead to eventual elimination of fish passage issues at Red Bluff by 

warranting the construction of a pumping plant capable of year-round operation. 

In FY 2002, a draft BA and a draft Environmental Impact Statement/Environmental Impact 

Report (EIS/EIR) for the RBDD Fish Passage Program Improvement Project were prepared and 

made available for public review. The document focused on structural alternatives for the 

solution of the fish passage problem at RBDD, and all would cost on the order of 80-100 million 

dollars for both fish passage improvements and the construction of an all-year round pumping 

plant. Work on these documents was suspended pending completion of a new ESA Section 7 

consultation on the OCAP for the CVP as a whole but is expected to be re-initiated in FY 2005. 

In FY 2004, the fourth pump was designed and the contract was awarded for installation. The 

pump is expected to be complete in FY 2006, with the components needed for successful water 

delivery and fish bypass to the river. 

In FY 2004, discussions on the various alternatives for solution of the fish passage/water 

delivery problems at RBDD by the Fish Passage Program’s Study Management Group 

continued. The Study Management Group consists of representatives from Reclamation, the 

Service, NOAA Fisheries, CDFG, and CDWR. Engineers from Reclamation’s Denver Technical 

Service Center made a site visit to the pumping plant to gather information for the preliminary 

design. 

Project Title: Clear Creek Restoration Program

 CVPIA Section 3406(b)(12) 

FY 2004 Funding: $579,193 

FY 2004 Accomplishments:

This section of the Act requires the restoration of Clear Creek, construction of a new fish ladder 

at the McCormick-Saeltzer Dam, and the development and implementation of a comprehensive 

program to provide flows to allow sufficient spawning, incubation, rearing, and outmigration 

for salmon and steelhead from Whiskeytown Dam. 

Since the removal of McCormick-Saeltzer Dam and its diversion from Clear Creek in 2000, 

efforts on Clear Creek have been re-focused on improvement of instream habitat conditions for 

anadromous salmonids. 
CVPIA – Annual Report for Fiscal Year 2004 32 

In FY 2004, the activities and accomplishments of the Clear Creek Restoration Program 

included: 

1. Implementation of the Clear Creek Stream channel restoration project. This project is 

restoring natural geomorphic form and process to the creek. Fisheries monitoring showed 

a 3.6 fold increase in Chinook salmon spawning density in the newly completed Phase 3A. 

In addition, migratory songbird diversity and population sizes are increasing in the 

restoration area. Topographic surveys and mercury characterization were conducted for 

Phase 3B. Mercury characterizations conducted by the University of Montana and the 

U.S. Geological Survey indicated that the project had no adverse impacts on mobilizing or 

increasing mercury concentrations in the creek. 

2. Implementation of salmon-friendly flows. These flows were partially responsible for the 

third highest fall-run Chinook salmon escapement on record. Recommendations for flows 

between June and September were suggested to maintain water temperatures that met the 

standards established by NOAA Fisheries for the protection of the endangered spring-run 

Chinook and steelhead. Recommendations were also made for flows between October 

and May to provide adequate spawning and rearing habitat for Chinook and steelhead. 

IFIM studies were used to determine long-term flows necessary to satisfy requirements of 

(b)(12). The Clear Creek Decision Analysis and Adaptive Management Model were 

improved to evaluate power, sediment, riparian and salmonid impacts from large 

managed releases of water. 

3. Implementation of the spawning gravel augmentation and monitoring program. 

Approximately 4,768 tons of spawning gravel was injected below Whiskeytown Dam. 

Monitoring indicated that federally listed as threatened spring-run Chinook salmon and 

steelhead were utilizing injected gravel for spawning areas. 

4. Continuation of Clear Creek monitoring efforts. Monitoring included juvenile salmonid 

use of restored habitats, fish stranding, adult population estimates, and redd mapping. 

Stream flows, water temperatures, spawning gravel, and stream substrate quality were 

also monitored in FY 2004. 

Project Title: Spawning Gravel Replenishment Program

 CVPIA Section 3406(b)(13) 

FY 2004 Funding: $675,673 

FY 2004 Accomplishments: 

The CVPIA directs that a program be established to replenish spawning gravels for 

anadromous fish that have been lost as a result of the construction and operation of the CVP, 

bank protection projects, and other activities on the Sacramento, American, and Stanislaus 

Rivers. The Spawning Gravel Replenishment Program has been established and, in the years 

since CVPIA enactment, has placed more than 135,000 tons of gravels in these streams to 

increase the availability of spawning gravel and rearing habitat for Chinook salmon and 

steelhead. In addition, existing gravel substrates on the American River have been ripped and 

manipulated to make them more usable for these purposes. 
CVPIA – Annual Report for Fiscal Year 2004 33 

Beginning in 1997, salmonid spawning gravel has been placed twice on the right bank of the 

mainstem Sacramento River immediately downriver from Keswick Dam, three times on the 

right bank immediately downstream from the confluence with Salt Creek, and once on the left 

bank on the Tobiasson property toward the southern extent of the Redding city limits. 

Subsequent high river flows dispersed the gravel downriver. Salmon have been observed on 

the restored habitat. 

The substrate at three riffles on the lower American River has been manipulated and salmonid 

spawning gravel subsequently placed at these sites in 1999 according to specifications. Salmon 

have been observed spawning on the restored habitat. Monitoring is under way to determine 

salmonid use of the gravel placed in the river. 

Also beginning in 1997, salmonid spawning gravel has been placed in the Stanislaus River at 

three different sites immediately downriver from Goodwin Dam. On two occasions, helicopters 

were used to deposit the gravel directly in the channel. This work was supplemented with 

gravel delivered by truck to areas adjacent to the channel, then pushed into the river channel. 

The gravel was subsequently dispersed downriver by streamflow. Salmon have been observed 

spawning on the restored habitat. Monitoring is under way to determine salmonid use of the 

gravel placed in the river. 

Accomplishments for the gravel replenishment program in FY 2004 include the following: 

1. Continued the monitoring program on the lower American River, documenting the use by 

salmon, the location of spawning redds, and the quality of treated versus untreated 

salmon spawning areas. 

2. Placed gravel in the Stanislaus River. The criteria for gravel cleaning and sorting, specific 

locations and timing of placement-related activities were determined as per approved by 

Service and CDFG biologists. 

3. Surveyed adult salmonid escapement both within and outside of the gravel placement 

sites in the Stanislaus River. Transects were made at all gravel placement sites both before 

and after gravel placement. 

4. Placed gravel in the Stanislaus River. A total of 1,155 tons of spawning gravel was placed, 

using a hydraulic placement technique. 

5. Placed gravel in the Upper Sacramento River. A total of 9,500 tons of spawning gravel 

was placed; 4,250 tons at the Keswick Dam site; and 4,250 tons at the Salt Creek site. 
CVPIA – Annual Report for Fiscal Year 2004 34 

Project Title: Comprehensive Assessment and Monitoring Program

 CVPIA Section 3406(b)(16) 

FY 2004 Funding: $220,179 

FY 2004 Accomplishments:

The CVPIA calls for establishing a comprehensive program to assess the biological results and 

effectiveness of CVPIA actions undertaken pursuant to subsection 3406(b) of the statute. In the 

past, the Comprehensive Assessment and Monitoring Program (CAMP) funded CDFG to 

perform a variety of monitoring efforts, including a summer Delta tow-net survey to provide 

information on American shad, elements of an adult striped bass monitoring program, juvenile 

salmonid out-migration monitoring on the Yuba, Merced, and Tuolumne Rivers, and a Central 

Valley angler survey focused on catches of Chinook salmon and steelhead. The latter is a 

necessary component of salmonid stock monitoring, along with spawning population surveys 

and ocean catch estimates provided by CDFG. 

Because of budget constraints, funding for the Delta tow-net survey and striped bass 

monitoring was discontinued in FY 2003. Funding for the juvenile studies on the Yuba, Merced, 

and Tuolumne Rivers had been discontinued the previous year. Lack of funding and the State 

budget crises combined to eliminate the Central Valley angler survey in 2004. 

Activities and accomplishments in FY 2004 were as follows: 

1. Closed out work on the Central Valley angler survey. The survey collected ongoing 

harvest data essential to determining anadromous fish production and, therefore, 

progress toward meeting CVPIA goals. It was funded by CAMP starting in 1998, but 

has been terminated as a result of budget re-prioritizations. 

2. Prepared a report on adult Central Valley Chinook salmon production estimates and 

juvenile emigration estimates for 2001 through 2003, using information that included 

prior Central Valley angler surveys. Results are mixed, with apparent population 

increases reported on Clear, Butte, and Battle creeks, and declines reported in some 

areas such as the San Joaquin River tributaries. Results will be posted on-line at the 

AFRP web site (http://www.delta.dfg.ca.gov/afrp/logopage.asp). 

3. Completed the second year of American River Chinook salmon and steelhead visual 

observation monitoring, which provided information for Folsom Dam operations and 

baseline data for future restoration projects. 

4. Funded a report on statistical procedures for assessing progress toward the AFRP 

Chinook salmon production doubling goal, and in determining sustainability of 

production increases. The report is to be used in further development of methods to 

assess population changes, and will be considered in fiscal year 2005 workshops on 

AFRP goals. 
CVPIA – Annual Report for Fiscal Year 2004 35 

Project Title: Glenn-Colusa Irrigation District Fish Screen Replacement 

Project

 CVPIA Section 3406(b)(20) 

FY 2004 Funding: $1,861,289 

FY 2004 Accomplishments: 

The CVPIA calls for elimination of loss or damage to fish in the Sacramento River from water 

diversion at Glenn-Colusa Irrigation District’s Hamilton City Pumping Plant. The plant diverts 

up to 3,000 cfs from the river, and past losses of fish at the facility have been very significant. A 

multi-agency/stakeholder effort to correct the problems has been under way for some time and 

all components of a state-of-the-art fish protection facility were completed in 2001. A five-year 

fish screen system testing/operation optimization program has been initiated. Transfer of the 

project to operations and maintenance status is scheduled for October 2007 provided the testing 

program finds the facility to be operating as designed. 

FY 2004 accomplishments include the following: 

1. Completed cost sharing agreements and transfer of funds. 

2. Continued hydraulic and biological testing of completed works. 

Project Title: Anadromous Fish Screen Program

 CVPIA Section 3406(b)(21) 

FY 2004 Funding: $8,035,796 

FY 2004 Accomplishments: 

The Anadromous Fish Screen Program (AFSP) serves two functions in its efforts to protect 

juvenile anadromous fish from the effects of water diversions. First, it is a source of funds to 

diverters to install fish screens or other protective devices at their facilities. As a matter of 

policy, cost-share funding is only provided for features of approved projects that are required 

for screening and protecting fish. Up to 50 percent of the funding for qualified features can be 

provided. The AFSP funds are expended on a biological priority basis and the AFSP is closely 

coordinated with the ERP, which is a potential source of additional funds for fish screen 

projects. 

Second, the AFSP Technical Team, with screen experts from various Federal and State resource 

and regulatory agencies, provides fish screen development guidance to the diverters 

participating in the AFSP, throughout the various phases of project planning and 

implementation. 

The AFSP has funded fish screen projects at water diversions, ranging from 17 cfs up to 1,000 

cfs, allowing diversions for authorized purposes while leaving juvenile fish in the waterway 

unharmed. Every project funded by the Program is a multi-year effort, with funds being 

provided for feasibility studies, engineering and design, construction, and then for start-up 

testing. Consequently, accomplishments reported in any given year may be the result of 

funding provided several years earlier. Through FY 2004, the AFSP has been responsible for the 
CVPIA – Annual Report for Fiscal Year 2004 36 

construction of 21 screens. Approximately 3,200 cfs of diverted water in Central Valley streams 

is now fish-safe as a result. Currently, the Program is involved with seven applicants, each in 

various phases of project development. 

Accomplishments in FY 2004 include the following: 

1. Continued screen design for Natomas Mutual Water Company (NMWC) unscreened 

diversions in Sacramento County for a total of approximately 630 cfs on the Sacramento 

River. 

2. Continued screen design for three Meridian Farms Water Company (MFWC) diversions 

that redirect water from the Sacramento River to irrigate 10,000 acres in Sutter County. 

3. Completed the City of Sacramento’s Sacramento River Water Treatment Plant 

Replacement Intake project which involved the construction of a new water intake on 

the Sacramento River approximately 750 feet downstream of the existing intake pier or 

1950 feet downstream of the American River confluence with the Sacramento River. 

4. Completed the modification of the City of Sacramento’s Fairbairn Water Treatment Plant 

located on the American River adjacent to California State University, Sacramento. 

Modification included replacing existing fish screens and adding new screens to comply 

with the fish screen criteria established by CDFG, the Service, and NOAA Fisheries. 

5. Continued design for construction of a fish screen structure for Reclamation District 

2035’s 400 cfs diversion on the Sacramento River, just upstream of the City of 

Sacramento. 

6. Continued design for construction of a fish screen structure for Patterson Irrigation 

District’s 190 cfs diversion on the San Joaquin River. 

7. Continued design for construction of a fish screen structure for Sutter Mutual Water 

Company‘s Tisdale Pumping Plant on the Sacramento River in Sutter County to replace 

two existing pumping plants. 

Project Title: Trinity River Restoration Program

 CVPIA Section 3406(b)(23) 

FY 2004 Funding: $8,879,207 

FY 2004 Accomplishments: 

The Trinity River Basin Fish and Wildlife Management Program was established by an act of 

Congress in 1984 to restore the fish and wildlife stocks in the Trinity River Basin that were 

adversely affected by the construction and operation of the CVP’s Trinity River Division. The 

program was fully functional until 1998 when Federal authorization and funding to develop 

and construct restoration measures expired. 

When the CVPIA was passed in 1992, it directed Interior, in Section 3406(b)(23), to complete the 

Trinity River Flow Evaluation Study mandated in 1981 and, under certain conditions, to 

implement the flows determined necessary for fishery restoration. The CVPIA, in Section 3406 

(b)(1), also directed the Secretary to address other identified CVP adverse environmental 

impacts, which includes the Trinity River Division. A Solicitor’s opinion in 1998 concluded 
CVPIA – Annual Report for Fiscal Year 2004 37 

that, absent reauthorization of the Trinity River Basin Fish and Wildlife Management Act of 

1984, the CVPIA provided sufficient authorization in those two sections, subject to certain 

limitations, to implement the resulting recommendations of the Trinity River Flow Evaluation 

Study report. 

The Trinity River Fishery Flow Evaluation Study report was completed in spring 1999 and an 

EIS/EIR was completed in October 2000. These documents analyzed a range of alternatives for 

restoring and maintaining the natural production of anadromous fish populations of the 

mainstem Trinity River downstream of Lewiston Dam. A final ROD was signed in December 

2000. The decision called for a range of flows from 369,000 af in critically dry years to 815,000 af 

in wet years to be released down the Trinity River. It also called for physical channel 

rehabilitation to accommodate the increased flows and to restore habitat components to 

accommodate the anticipated increased fish returns. However, due to litigation, Interior is 

currently limited to restoration actions that are not flow related. 

In order to implement the increased instream flows, it was determined that modifications to 

four existing bridges needed to be made. Because of the association with the CVPIA mandate to 

implement the results of the flow study, this work was determined to fall within the scope of 

the CVPIA. Planning and design began in FY 2001, and they were funded by CVPIA. 

FY 2004 accomplishments include the following: 

1. Finalized design and construction specifications for Salt Flat, Biggers Road, Bucktail and 

Poker Bar. Construction of replacement bridges at Salt Flat, Biggers Road, and Poker Bar, 

and raised approach construction at Bucktail Bridge. 

2. Finalized design and initiation of construction of bank rehabilitation and floodplain 

restoration at Hocker Flat and other locations. 

3. Rehabilitated the floodplain and channel connection with the enhancement of geomorphic 

and biological features. Increased geomorphic and hydraulic complexity to provide 

greater diversity of fish habitats capable of supporting a wide range of life history stages. 

4. Revegetated native riparian habitat adjacent to constructed bridges and at rehabilitation 

sites. Also modified the distribution of riparian vegetation to benefit fish and wildlife 

species. Riparian vegetation was removed from channel margins and was restored in 

floodplain areas. 

5. Completed flood inundation mapping to inventory and analyze all floodplain structures 

potentially at risk between Lewiston Dam and the North Fork Trinity River. 

 
CVPIA – Annual Report for Fiscal Year 2004 38 

Project Title: Refuge Water Supply Program – Water Conveyance Component

 CVPIA Section 3406(d)(1-5) 

FY 2004 Funding: $7,714,118 

FY 2004 Accomplishments: 

The CVPIA directs Interior to provide long-term, reliable water supplies to Central Valley State 

and Federal refuges, to the Grassland Resource Conservation District, and to certain lands 

identified in the “San Joaquin Basin Action Plan/Kesterson Mitigation Action Plan Report” 

(referred to as the San Joaquin Basin Action Plan lands). The Act authorized such water to be 

provided from CVP supplies and from water acquired by the Water Acquisition Program 

established pursuant to Section 3406(b)(3). The Act also authorized Interior to construct 

facilities as necessary to deliver the water to the various refuge units and/or to acquire the 

conveyance capacity from non-Federal entities for them to convey the water to the refuge areas. 

The Refuge Water Supply Program consists of three separate but highly coordinated 

components to deliver the water supplies to the identified refuges. These are the Water 

Conveyance “Wheeling” Component to acquire conveyance capacity from non-Federal entities 

and two construction components. The Facilities Construction Component constructs needed 

facilities to deliver water to the State and Federal refuges, and the San Joaquin Basin Action 

Plan Construction Component constructs the facilities necessary to deliver water supplies to the 

San Joaquin Basin Action Plan lands. 

The Water Conveyance “Wheeling” Component conveys prescribed quantities to refuge areas 

not having their own delivery facilities through cooperative agreements with wheeling entities 

that have conveyance capability. As of the end of FY 2004, nine long-term (25-30 year) 

conveyance cooperative agreements (wheeling agreements) were in place and being used to 

deliver water to certain refuges. These long-term agreements are with San Luis Canal Company 

(two agreements), Biggs-West Gridley Water District, Central California Irrigation District, 

Grassland Water District, San Luis Delta Mendota Water Authority, Buena Vista Water Storage 

District, Tehama-Colusa Canal Authority, and the Glenn-Colusa Irrigation District. 

FY 2004 funds were generally expended to negotiate and implement wheeling agreements and 

to coordinate the overall Refuge Water Supply Program, including evaluating the various 

alternatives for delivery of water to the refuge areas. 

FY 2004 activities and accomplishments of note include the following: 

1. Worked with the Interagency Refuge Water Management Team to develop Level 2 and 

Level 4 water delivery schedule scenarios, expedite refuge monthly water delivery 

schedules, and prioritize the distribution of limited Level 4 water supplies. 

2. Conveyed approximately 100 percent of Level 2 water supplies in both the Sacramento 

and San Joaquin Valleys. For Level 4 water, the program conveyed approximately 6,300 af 

in the Sacramento Valley and approximately 70,000 af in the San Joaquin Valley. 

3. Coordinated with CVO, the Water Acquisition Program, and the refuges on water needs 

and delivery schedules to ensure the contract obligations were met. CVO was responsible 
CVPIA – Annual Report for Fiscal Year 2004 39 

for providing Level 2 water supplies and the Water Acquisition Program component was 

responsible for acquiring Incremental Level 4 supplies. 

4. Continued participation in the long range planning study “Evaluation of Groundwater 

Potential for Level 4 Refuge Water Supplies”. This study was issued in July 2004, and 

identified groundwater data needs, refuges with the highest potential to use onsite 

groundwater to meet Level 4 water needs, and potential short-term and long-term 

implementation. 

5. Initiated development of refuge water quality goals and a programmatic monitoring 

program. 

6. Continued negotiation of a new 5-year contract with CDWR for conveying water to the 

Kern National Wildlife Refuge. 

7. Continued development of an integrated database for refuge water supply accounting, 

delivery scheduling, tracking and invoicing. 

8. Continued development of a report highlighting specific biological benefits documented 

on refuge units since the implementation of the refuge provisions in CVPIA. 

9. Continued coordination with the staff from CALFED’s Water Use Efficiency Program and 

the California State University-San Luis Obispo to install water monitoring and 

conservation equipment at the Kern National Wildlife Refuge on a trial basis. 

10. Completed the installation of new water measurement devices for the San Luis National 

Wildlife Refuge through a cooperative effort with the Grassland Water District. 

11. Completed the draft Criteria for Refuge Water Management Plans (Criteria). The draft 

Criteria were published in the Federal Register on June 28, 2004 for a 30 day public review 

and comment period. 

Project Title: Refuge Water Supply Program – Facilities Construction 

Component

 CVPIA Section 3406(d)(1-5) 

FY 2004 Funding: $3,618,578 

FY 2004 Accomplishments:

The facilities construction component of the Refuge Water Supply Program was developed to 

provide the necessary infrastructure to support the long-term delivery of firm, reliable water 

supplies to specific State and Federal refuges in the Central Valley. These refuge units are 

Sacramento, Delevan, Colusa, Sutter, Kern, and Pixley National Wildlife Refuges and the State’s 

Mendota and Gray Lodge Wildlife Areas. 

To date, construction of the necessary facilities to transport water supplies to the Sacramento, 

Delevan, Colusa, and Kern National Wildlife Refuges has been completed. This effort includes 
CVPIA – Annual Report for Fiscal Year 2004 40 

negotiating and awarding Facilities Construction Agreements with water purveyors to design 

and construct approximately 150 facilities. Also included in this effort was the fulfillment of 

environmental commitments pursuant to the Service’s ESA BO for construction of conveyance 

facilities for the West Sacramento Valley Study Area (Sacramento Deleven, and Colusa National 

Wildlife refuges), East Sacramento Valley Study Area (Sutter National Wildlife Refuge and the 

Gray Lodge Wildlife Area), the South San Joaquin Valley Study Area (Kern and Pixley National 

Wildlife Refuges), and the Mendota Wildlife Area. 

FY 2004 accomplishments include the following: 

1. Continued on-going development of the environmental documentation for Mendota 

National Wildlife Refuge. Negotiations of the Facilities Construction Agreement for 

Mendota infrastructure will be initiated and finalized in FY 2005. 

2. Completed designs/specifications and construction activities pursuant to the provisions 

in the Facilities Construction Agreement with Buena Vista Water Storage District to 

provide infrastructure to Kern National Wildlife Refuge. 

3. Initiated the Facilities Construction Agreement with Biggs-West Gridley Water District to 

provide infrastructure to Gray Lodge National Wildlife Refuge. The Facilities 

Construction Agreement (designs/specifications and construction) is expected to be 

completed in FY 2008. 

Project Title: Refuge Water Supply Program – San Joaquin Basin Action 

Plan Component

 CVPIA Section 3406(d)(1-5) 

FY 2004 Funding: $1,027,544 

FY 2004 Accomplishments: 

Environmental documentation for implementation of the San Joaquin Basin Action Plan was 

completed in 1997. An Implementation Plan was completed in April 1998, and cooperative 

agreements with the San Luis Canal Company, Grassland Water District, and Central California 

Irrigation District to convey water to the Action Plan lands were completed in summer 1998. 

Reclamation is currently administering the cooperative agreements, which include construction 

and rehabilitation of facilities to accommodate the needs of the refuges within San Joaquin 

Basin Action Plan area. Reclamation is completing design and construction work for the 

remaining facilities identified in the Implementation Plan. Construction of these facilities is 

ongoing and is expected to continue through FY 2006 and beyond, depending on the level of 

future funding. 

As part of these efforts, the Grassland Water District’s San Luis Spillway Ditch was increased 

from its previous capacity of 300 cfs to 350 cfs in order to accommodate the delivery of water to 

wetland habitat in the Grassland Resource Conservation District and portions of the San Luis 

National Wildlife Refuge. The San Luis Spillway Headworks also required modification in 

order to accommodate the additional flows through the District’s canal. The original structure 

included one 24-inch and three 54-inch pipes and slide gates that restricted flow to less than the 
CVPIA – Annual Report for Fiscal Year 2004 41 

required 350 cfs. Reclamation designed a new Radial Gate Control Structure and a contract for 

removal and disposal of the existing structure and a contract for construction of the new 

structure was awarded in FY 2001. However, the contractor, Zerimar Corporation, defaulted 

before commencing construction, which delayed the project completion one year, FY 2003. 

FY 2004 accomplishments include the following: 

1. Continued progress on capacity and efficiency improvements to Central California 

Irrigation District (CCID) facilities. Under the existing cooperative agreement with CCID 

the Cottonwood Lateral was completed for the conveyance of refuge water to the 

Grassland Resource Conservation District from CCID’s Main Canal. Funding was 

provided for the enlargement of the O’Banion Bypass to transfer CCID’s Outside Canal 

water to the CCID’s Main Canal, Helm Turnout, and Ora Loma Weir. 

2. Continued work on the EA for the proposed delivery alternatives for the East Bear Creek 

Unit of the San Luis National Wildlife Refuge. This effort was contracted in 2002 with 

CH2MHill, Sacramento, California. Design data collection for the preparation of design 

and specifications for the conveyance facilities was also completed. 

Project Title: Ecological/Water Systems Operations Models Development 

Program

 CVPIA Section 3406(g) 

FY 2004 Funding: $715,690 

FY 2004 Accomplishments: 

The Ecological/Water Systems Operations Models Development Program is a continuing effort 

initiated in 1994. The program supported: 

1. The Ecosystem Modeling Consensus Project, designed to identify needed development of 

a credible and consistent set of tools to support management decisions involving water 

and biological resources. 

2. Review and update of the Central Valley Ground-Surface Water Model. 

3. Development of a graphical user interface and database for the PROSIM and SANJASM 

models (note: This effort was abandoned because the CALSIM model replaced both 

PROSIM and SANJASM). 

4. Development of the 3-D temperature model for Whiskeytown Reservoir. Development of 

the CALSIM II model and hydrologic input for CALSIM. 

Since 1998, this program has provided a steadily increasing level of support for development 

and application of CALSIM II. Reclamation and CDWR have made a major commitment to 

CALSIM and it is essential for Interior to participate in and guide its development and 

application. CALSIM II is now available for public use and has been applied to water supply 

improvement studies. The Ecosystem/Water System Model Development Program continued 
CVPIA – Annual Report for Fiscal Year 2004 42 

through FY 2004 to provide the basic support for continuing CALSIM II development and 

distribution to a wide range of users. 

The Ecological/Water Systems Operations Models Development Program is also involved in 

the development of new reservoir and river temperature models to be used for operations and 

planning. Part of this effort includes ensuring that appropriate staff is capable of implementing 

these models. Reclamation, the Service, CDWR, and private contractors all have staff capable of 

applying these models that have been trained under funding from this program. 

Accomplishments include the following: 

1. Continued oversight and review of CALSIM. 

2. Continued review and documentation of CALSIM II code. 

3. Continued development of a Graphical Information System (GIS) representation of 

CALSIM II coverage. 

4. Continued hydrology documentation for the San Joaquin Valley. Work was originally 

initiated in FY 2002 but was not funded until FY 2003. 

5. Held a three day workshop in Sacramento on the application of the 2-D reservoir and river 

temperature model CE-QUAL-W2. 

6. Continued management of CALSIM II and river and reservoir water temperature 

simulation. 

7. Supported Reclamation participation in the joint, with CDWR, Climate Change Work 

Team. 

8. Supported Service participation in review and development of CALSIM II. 

9. Participated in Professional Organizations including the California Water and 

Environmental Modeling Forum and conferences with organizations such as American 

Society of Civil Engineers and American Water Resources Association. 

Project Title: Land Retirement Program

 CVPIA Section 3408(h) 

FY 2004 Funding: $1,586,410 

FY 2004 Accomplishments: 

The CVPIA authorizes Interior to acquire irrigated agricultural lands that are drainageimpaired and receive CVP water. These lands are then retired them from agricultural 

production. The CVPIA Land Retirement Program was established to implement this 

provision. The main goals of the CVPIA Land Retirement Program are: 
CVPIA – Annual Report for Fiscal Year 2004 43 

1. to improve water conservation by district, or improve the quality of an irrigation district’s 

agricultural wastewater, 

2. to reduce drainage and improve water quality in the San Joaquin River, and 

3. to use retired lands to create additional wildlife habitat in the San Joaquin Valley 

In FY 2004, the CVPIA Land Retirement Program, at both its sites in Tranquillity and Atwell 

Island, continued acquisition, research, restoration, site management, reports, and outreach. 

Acquisitions for the Land Retirement Demonstration Site at Atwell Island continued to finalize 

transactions to reach the goal of 8,000 acres. During FY 2004, 30 acres were purchased and an 

additional 154 acres are expected to close by end of FY 2004. Other acquisition actions began 

with the acceptance of an Interior offer for a 625 acre parcel. In addition, an appraisal is 

currently underway for a 160 acre parcel. 

The following are research accomplishments for FY 2004:

 

1. Completed data collection for the 5-year Habitat Restoration Study, designed to determine 

the effects of habitat restoration on wildlife on 20, 10-acre plots at the Tranquillity study 

site. 

 

2. Entered all data into databases, proofed, edited and a suite of exploratory data analysis 

and graphing accomplished for selected data sets covering the 5 consecutive years of the 

study (1999 to 2004). 

3. Conducted restoration research trials on 64 plots on 15 acres at Tranquillity and interplanted on 20 acres of alfalfa at Atwell Island. ESRP and BLM staff assisted Reclamation 

to design and establish sample plots containing eight native plant species planted with a 

variety of techniques. 

4. Continued soil and groundwater monitoring at both LR Demonstration Project sites. 

5. Purchased monitoring equipment to gather weather data at Atwell Island site to be 

integrated into California Irrigation Management Information System (CIMIS). 

6. Developed a conceptual model of groundwater flow at Tranquillity site in preparation for 

a numerical model simulating groundwater response to land retirement. 

The following are restoration efforts & site management accomplishments for FY 2004:

 

1. Expanded the San Joaquin Valley native plant nursery at Tranquillity to 5 acres and 

increased from 34 to 64 species (13 shrubs, 30 annual herbs, 19 perennial herbs, 2 perennial 

grasses). Collections of 91 species from 78 locations were made on 314 collecting trips. 

Additionally, 8 species were established in 0.5 acre plots using mechanized production 

and harvesting methods. Mechanized seed cleaning equipment was purchased and 

operations established. Large quantities of seed were collected under seed collecting 

contracts. An established 1.5 acre grow-out area for native grass seed is under contract for 
CVPIA – Annual Report for Fiscal Year 2004 44 

alkali sacaton. Continuation of research on seed delivery, plant propagation, and seed 

production methods with the USDA Plant Material Center in Lockeford, California. Seed 

augmentation of three targeted species will be conducted in FY 2005. 

2. Accomplished restoration and site management activities at both Tranquillity and Atwell 

Island with cooperating farmers. Barley was planted at Tranquillity on 600 acres in 

buffers that isolate the study plots from one another, inhibit the establishment of weeds, 

and reduce erosion and dust. Additionally, barley was planted on 120 acres that was 

previously used as research trials, so that new trials can be installed in FY 2005. On 80 

acres, a new cultivar of barley (UC937) developed by UC Davis for use on high saline soils 

was planted. Establishment of 32 miles (80 acres) of native hedgerows at Atwell Island. 

Seeding occurred on 20 acres of range land after treatment with a propane flamer. Iodine 

bush was seeded on 7 acres of a sump (former evaporation pond). A mix of native 

annuals and perennials was planted on an additional 20 acres. A hydro-planter installed 

100 tree cuttings in riparian-canal areas along with 25 potted trees and shrubs. 

3. Established a diversified upland habitat at Atwell Island as a wildlife farming 

demonstration area with 15 acres of native shrub plantings interspersed with 20 acres of 

crops, 5 acres each of vetch, milo, maze, wheat, and safflower. The results of this wildlife 

habitat planting laid the groundwork for a Cooperative Agreement with the Westside 

Resource Conservation District to implement five units in Fresno County in FY 2005. 

Management of the existing 20 acre wetland at Atwell Island for wintering waterfowl. 

Cooperation with the USDA-NRCS of Visalia led to establishment of a wetland for 

breeding season waterfowl and shorebirds on an adjacent 10 acres. 

Reports and Recovery Implementation Plans for Upland Species in FY 2004 included the 

following: 

1. Published the Fourth Annual Report for the Land Retirement Demonstration Project in 

January 2004.

2. The Five-Year Land Retirement Demonstration Project Report (1999-2004) will be available 

for review by October 2004. For the Tranquillity site of the CVPIA Land Retirement 

Program Demonstration Project, this report will fulfill the five years of monitoring 

requirements pursuant to the Service’s ESA BO September 1999.

3. Developed an Implementation Plan for recovery of upland species on restored retired 

agricultural lands began in FY 2004. Updates by subject experts of listed species’ habitat 

requirements form the basis for discussions of how to best utilize the techniques and 

native plant species of the CVPIA Land Retirement Program for upland habitat restoration 

on retired agricultural lands. Such restoration could contribute, possibly substantially, to 

upland species recovery. Information will be collected in FY 2004 and the Implementation 

Plan written and reviewed in FY 2005. 
CVPIA – Annual Report for Fiscal Year 2004 45 

Outreach accomplishments for FY 2004 included the following:

1. Presentations and posters were given at a number of forums in FY 2004. These included: 

Annual Statewide CDWR Workshop, Drainage and Salinity Annual Conference, 

American Society of Mammalogists, California Native Plant Society, Society of Ecological 

Restoration and the Raptor Research Foundation. 

2. Outreach to the local high school science classes and science clubs introduced a workshop 

on land retirement that included classroom and on-site field work. A volunteer day at the 

native plant nursery was held in observance of Earth Day. Two CSU Fresno graduate 

students are conducting research at the Tranquillity site. They are investigating the 

population structure of native plant pollinators and seed delivery methods for 7 native 

plant species. A graduate student from CSU Fresno is studying the effects of post-harvest 

flooding at Atwell Island. 

3. Partnerships were fostered by participation in the Tulare Lake Basin Working Group. 

Partnerships have been developed with Sequoia Riverlands Trust; Tulare County 

Audubon Society; USDA-NRCS; and the Service. 

DISCUSSION OF CVPIA IMPLEMENTATION AND RESULTS 

Fiscal year 2004 was the 12th year since passage of the CVPIA. Over this period, hundreds of 

actions have been taken to meet the Act’s goals and objectives. Many of these actions were 

procedural and, once implemented, fulfilled the statute’s requirements. For other provisions, 

particularly the fish and wildlife measures, progress towards attaining CVPIA goals and 

objectives has been more gradual. Measuring progress towards attaining these goals and 

objectives has been a challenging task. The long-term, system-wide results of implementing 

individual actions, or of multiple actions within any single year, may not be seen for many 

years and when apparent, may not be directly attributable to any particular action but rather to 

a suite of actions taken by multiple programs over a long period of time. Consequently, 

reporting the response of the ecosystem to actions implemented in any particular year and then 

separating that response from results of work done in previous years is not practical. This is as 

true for FY 2004 as it has been for any of the previous 12 years of CVPIA implementation. 

Nevertheless, we believe target fish and wildlife resources are responding to CVPIA measures. 

The long-term programs and plans developed to achieve goals and objectives of the CVPIA are 

gradually being realized. The numbers of salmon returning to the Central Valley are increasing. 

Salmon have returned to spawn in areas where they have not been seen for many years. 

Hundreds of thousands of ducks, geese and other migratory birds are using wetlands areas 

newly created or greatly enhanced as a result of CVPIA programs. Avian diseases throughout 

the valley have declined. Tens of thousands of acres of habitat has been acquired for threatened 

and endangered species and thousands more has been restored and/or enhanced, clearly 

benefiting species on the brink of extinction, increasing their chances for recovery. 

To better identify progress towards meeting CVPIA goals, the Restoration Fund Roundtable 

tasked a subcommittee to engage with Reclamation and the Service in an effort to evaluate 
CVPIA – Annual Report for Fiscal Year 2004 46 

CVPIA programs. The resulting “Program Evaluation” process includes identifying objectives 

of CVPIA programs, clarifying measurable outcomes, and evaluating progress. Thus far, 

Reclamation and the Service have focused on four programs as a pilot to test this process: the 

Clear Creek Restoration Program, the Spawning Gravel Replenishment Program, the AFRP, and 

the AFSP. For the Clear Creek Restoration and Spawning Gravel Replenishment programs, 

draft documents have been produced that detail objectives, outcomes, and progress. The 

Restoration Fund Roundtable has provided feedback, and the documents are continually 

improving. Current planning is underway for the AFRP and the CALFED Science Program to 

hold a joint workshop during the summer of 2005 to address anadromous fish restoration 

issues. Finally, to identify the extent that screening diversions is necessary in the Central 

Valley, the AFSP has convened a Fish Screen Program Evaluation Committee. This committee 

meets monthly, and is comprised of representatives from the Service, Reclamation, CDWR, 

CDFG, NOAA Fisheries, ERP, and the ERP Science Board. Through the use of models and 

monitoring of juvenile anadromous fish loss in diversions, this committee hopes to gain an 

understanding of the impact that diversions have on anadromous fish populations, and using 

that information, develop screening criteria to minimize that impact. 

Anadromous Fish - Biological Response 

Chinook salmon continue to be a high priority for CVPIA restoration efforts. A majority of 

implemented measures and the $459 million expended to benefit anadromous fish over the past 

12 years has been focused on this species. While the numbers of salmon along the West Coast 

have declined, adult returns to the Central Valley and the catch off the California coast have 

increased overall, correlating well with implementation of CVPIA measures since 1993. Even 

though other factors such as hydrology, ocean conditions, and fishing regulations have 

undoubtedly had some effect, the other declining west coast salmon fisheries have been subject 

to these same factors as well. 

Clear Creek provides a good example of positive biological gains correlating closely with 

CVPIA-related efforts. On Clear Creek, streamflows were increased during critical periods for 

fall-run Chinook salmon; spawning gravel was added to the stream; degraded portions of the 

stream channel, floodplain, and adjacent riparian habitats were restored; and erosion and 

sedimentation from sources within the watershed were controlled. McCormick-Saeltzer Dam, a 

major impediment to upstream passage of salmon and steelhead, and an associated unscreened 

diversion that reduced flows in the lower portions of the creek, have been removed. 
CVPIA – Annual Report for Fiscal Year 2004 47 

 

The fall-run Chinook salmon runs in Clear Creek increased greatly following implementation of 

these measures. Spawning production of fall-run Chinook salmon in Clear Creek, which in 

1952-1991 averaged 4,625 fish, increased to an average of 11,515 fish in 1992-2003. Furthermore, 

the improvement in flows and removal of McCormick-Saeltzer Dam opened Clear Creek to use 

by steelhead and spring-run Chinook salmon, both threatened species. Adult returns over the 

next several years should indicate whether there will be significant increases in numbers of 

these special status species and indicate whether or not the fall-run response is a long-term 

upward trend induced by CVPIA actions or just a temporary or cyclical increase resulting from 

other factors. At this time, the results are very encouraging. 

Very positive biological gains have occurred on several other streams where CVPIA efforts have 

been focused. Notable among these is Butte Creek, where spring-run Chinook returns have 

been steadily improving. Butte Creek spring-run natural production, which averaged only 

2,231 fish from 1960-1991, increased to an average of 14,350 fish since 1995 (1995-2003) when 

Butte Creek restoration measures were implemented. 

Natural production of salmon on several Central Valley streams, in some years, has reached or 

exceeded levels twice the average between 1967 and 19911. To determine if this increased 

natural production is sustainable on a long-term basis, several life cycles (three to five years per 

cycle) of continued monitoring would be necessary under a variety of environmental 

conditions. In addition, there are many other streams where the production of salmon and 

other anadromous fish are still declining. 

 

1 The CVPIA goal for AFRP is to ensure that the natural production of anadromous fish in Central Valley 

rivers and streams be sustainable, on a long-term basis, at levels at least double the average that existed 

during the 1967-1991 baseline period. A statistical process is being developed to assist in determining the 

sustainability of increased population levels. 
CVPIA – Annual Report for Fiscal Year 2004 48 

In those Central Valley rivers and streams with 

sufficient data, Figure 5 presents natural 

production of Chinook salmon for the period of 

CVPIA implementation (1992-2003) as a 

percentage of twice the average production 

during the baseline period (1967-1991). For 

example, Figure 5 shows natural production of 

Clear Creek fall-run Chinook salmon to be 

172% greater than twice the baseline 

production. If Clear Creek fall-run Chinook 

salmon numbers are shown to be sustainable, 

then the sustainable doubling goal could have 

been exceeded by 72% for this run on Clear 

Creek. Likewise, production for Yuba River 

fall-run is 67% of twice the baseline production, 

or 33% below this level and 17% above the 

1967-1991 average production. In contrast, 

production for Tuolumne River fall-run is 29%, 

or 71% below twice the baseline production 

and 21% below the 1967-1991 average 

production. Natural production was calculated 

based on escapement data compiled by the 

California Department of Fish and Game in 

their GrandTabdatabase2 and using methods 

described in Appendix A of the Final 

Restoration Plan for the Anadromous Fish 

Restoration Program (USFWS, 2001)3. Several 

small streams and two rivers identified in the 

Final Restoration Plan are not included in this 

figure due to insufficient data4. Five of the 21 

populations of Chinook salmon in Figure 5 

have exceeded the numeric doubling goal and 

13 (including these 5) have exceeded 

production for the baseline period. As stated 

earlier, continued monitoring will be necessary 

to determine if these production levels are 

sustainable on a long-term basis. 

 

2 Because numbers associated with this process include estimates, there are inherent sample errors. 

3 U.S. Fish and Wildlife Service, 1995. Working paper on restoration needs: Habitat restoration actions 

to double natural production of anadromous fish in the Central Valley of California. Volumes 1-3. May 

9, 1995. Prepared for the U.S. Fish and Wildlife Service under the direction of the Anadromous Fish 

Restoration Program Core Group. Stockton, CA. 

4 Cow Creek, Paynes Creek, Antelope Creek, Miscellaneous small creeks, Big Chico Creek, Bear River 

and the Calaveras River were not included. 

Figure 5 
CVPIA – Annual Report for Fiscal Year 2004 49 

Refuges and Waterfowl – Biological Response

With the passage of CVPIA, a firm and reliable water supply was made available to Central 

Valley State and Federal refuges, and private wetland areas. Flooding waste grain agricultural 

fields during the winter provided new seasonal habitats for waterfowl. Waterfowl, shorebirds, 

and other wetland-dependent wildlife benefited from the expansion and enhancement of 

habitat. Valley refuges reported increases of thousands of acres of new wetland habitats and 

tens of thousands of acres of enhanced habitats as a result of CVPIA water supplies. These 

refuges provided habitat for longer periods during the year, providing refuge managers with 

the ability to manage a much more diverse mix of habitat types that more fully satisfied the 

year-round environmental requirements of many wildlife species. Prior to CVPIA, refuge 

managers had to concentrate the vast majority of their water use in the fall and early winter 

months, when Central Valley waterfowl numbers peaked. With the passage of CVPIA, the 

habitat calendar was expanded to the full year. Under CVPIA, moist soil food plant irrigations 

are carried out; water is available during August and September to satisfy the needs of the first 

wintering ducks and geese that arrived in the Central Valley; maintenance flows are applied 

throughout the winter months to improve water quality and decrease avian disease outbreaks; 

and spring and summer water provided critical nesting habitat for waterfowl and colonial 

birds. 

 

Water availability also enhances refuge managers’ ability to provide a food supply for the 

winter migrants. Waterfowl food production increased tenfold in some refuge areas. The 

Grasslands Resource Conservation District (RCD) increased its acreage of enhanced seed 

production from 4,000 acres in 1991-92 to an average of 26,000 acres from 1993 to 2004. In that 

same time period, plant biomass doubled per acre. 

Waterfowl use increased nearly as much. In the Grasslands RCD, waterfowl use in the early fall 

increased by 300 percent. Other areas recorded increases of 800 percent, from 2 million to over 

18 million waterfowl use days per year. Not only has waterfowl use increased, but visits to 

these areas by the public have increased as well, drawn by the prospect of seeing hundreds of 

thousands of birds of many species at one time in a far more natural setting than was previously 

possible. 

Additional refuge water supplies provided by CVPIA have helped to alleviate waterfowl 

overcrowding, particularly in the Sacramento Valley. Waterfowl disease-related mortality, 

usually caused by overcrowding and stagnant water, decreased markedly in the valley as birds 

took advantage of the increased habitat and improved water quality. Cholera outbreaks, once 

frequent and widespread in the Sacramento Valley, have been reduced to one major incident 

since the passage of CVPIA. Similarly, the Sacramento NWR complex reported a nearly 89 

percent decline in botulism since 1992, compared to the decade prior to the availability of 

CVPIA water supplies. 

Species other than waterfowl benefited from CVPIA water. Sacramento Valley refuges reported 

an increased presence of western pond turtles and colonial nesting birds, such as the tri-colored 

blackbird. In fact, the largest tri-colored blackbird colony documented in California in 2004 

occurred at Delevan NWR, a population of over 75,000 individuals. In addition, refuges in the 

San Joaquin Valley noted increases in populations of giant garter snake and in nesting western, 
CVPIA – Annual Report for Fiscal Year 2004 50 

Clark’s, and eared grebes; black-crowned night herons; and tri-colored blackbirds. Valley-wide, 

shorebird use on shallow wetlands increased by hundreds of thousands as sandpipers, dunlins, 

yellowlegs, phalarope, and dowitchers responded to the increased wetland acreage and 

subsequent invertebrate food supplies. More than 150 species of other birds, 20 species of 

butterflies, 15 species of dragonflies, 5 species of reptiles, 2 species of amphibians, and 10 

species of mammals were reported using these enhanced habitat areas in the North Grasslands 

Wildlife Area alone. 

White-faced ibis and sandhill cranes are excellent examples of how the availability of adequate 

water supplies enabled refuge managers to provide habitat for endemic species that had been in 

severe decline for decades. Improved water supplies first led to an increase in the numbers of 

frogs, snails, aquatic insects, and small fish. This, in turn, provided the ibis and cranes with 

habitat for late-spring and summer nesting, essential components for these species. The 

increased and improved breeding habitat resulted in a steady upswing in bird numbers. Sutter 

NWR, for example, hosted 100 white-faced ibis in 1991. That number increased to 1,000 birds in 

2000, 7,000 in 2001, and a staggering 15,000. Kern NWR had a similar experience, with 50 ibis in 

1991, 5,600 in 2001, and over 8,000 in 2004. Pixley NWR supported 200 sandhill cranes in 1992 

when the CVPIA was passed. It received its first allocation of CVPIA water in 1993 and 

provided habitat for more than 2,000 cranes that year. By 2001, the number rose to 5,100 

sandhill cranes and has remained over 5,000 ever since. 

Other Fish and Wildlife – Accomplishments

Efforts under the CVPIA since 1993 to protect and provide habitat for fish and wildlife species 

other than anadromous fish and wetland-dependent wildlife have resulted in the acquisition of 

more than 98,179 acres from willing sellers at fair market prices, and the restoration of 1,111 

acres of native habitat for special status species. This includes fee acquisitions as well as 

conservation easements and was usually accomplished through partnerships with others such 

as TNC and TPL. These lands are now protected from the adverse impacts that would have 

occurred if they were developed. Nearly 8,300 acres of drainage impaired agricultural lands 

have been retired from irrigated agriculture, 2,411 acres of which has been treated to begin the 

process of restoration of upland habitat characteristics. Desirable plant and animal habitats 

along the San Joaquin River from Friant Dam to the river’s confluence with the Merced River 

are being enhanced. Over the next several years, we anticipate that the populations of species 

associated with these habitats, and particularly those that are considered threatened or 

endangered, will increase substantially. 

The CVPIA Land Retirement Program Demonstration Project experience is perhaps indicative 

of the benefits that we expect to achieve. Preliminary monitoring results from the Westlands 

site indicate a decline in the shallow groundwater table in response to land retirement, which is 

important as the highly saline groundwater has high concentrations of selenium and boron. 

Restoration of these retired lands and their use by wildlife however, has not resulted in 

increased levels of bio-accumulated selenium. Selenium concentrations in vegetation, 

invertebrates and mammals have not changed significantly over the study period to date. All 

selenium levels measured are considered below concentrations of concern to EPA and the 

Service. 
CVPIA – Annual Report for Fiscal Year 2004 51 

Treating these lands has increased abundance and diversity of wildlife. Increased invertebrate 

species and abundance include parasites and predators of agricultural pests as well as beneficial 

pollinators. Bird species diversity and abundance increased across all treatments immediately 

following restoration efforts. Recorded at the Demonstration Project site in Fresno were 17 

special status avian species. Populations of small mammals increased substantially on retired 

lands. Three special status mammalian species colonized restored land at Atwell Island, 

including the San Joaquin kit fox, observed using the 80 acres of hedgerows established this 

fiscal year. Native seed supplies necessary for successful restoration are being secured in four 

ways: (1) a native plant nursery is propagating 91 species collected from 78 sites; (2) an organic 

farmer is growing two perennial grasses; (3) natives from remnant populations are being 

gleaned through seed collection contracts; and (4) seed augmentation and propagation are 

being done through an MOU with the USDA Plant Material Center in Lockeford, CA. 

CONCLUSIONS 

Quantifiable Progress In 2004

At the conclusion of 2004, significant progress has been made in meeting CVPIA’s fish and 

wildlife goals. This progress includes, on some watersheds, nearing the dominant target of 

seeking to double anadromous fish numbers in the Central Valley system and in restoring and 

invigorating other species at risk. In the first decade since the CVPIA was enacted, a vast 

amount of essential “foundation work” has taken place. Foundation work is essential to the 

final outcome, but often not highly visible. It involves many activities -- data collection, 

research, development of alternatives, alternatives analysis and feasibility studies, permitting 

and design work. Adequate foundation work is critical if the desired outcomes (CVPIA’s 

purposes) are to be achieved: (a) fish and wildlife protection, restoration and enhancement; 

(b) addressing CVP impacts; (c) improving CVP operational flexibility; (d) expanding water 

transfers; (e) protecting the Bay/Delta; and (f) achieving a reasonable balance of CVP water 

uses. Much of that work has been accomplished, although more must continue. 

In 2004, some significant “on the ground” achievements were made toward the overall 

environmental goals of the CVPIA. The achievements, and the promise for similar 

achievements in the future, create a level of optimism that the CVPIA can achieve its 

environmental goals within a reasonable period of time and with reasonable expenditures. 

One of the most significant events through 2004 has been the increase of anadromous fish 

populations in five different Central Valley tributary streams (Figure 5, page 48). Most notable 

is the Butte Creek spring-run Chinook salmon, whose population has increased to an 

astonishing 563 percent of twice its average 1967-1991 natural production, the numeric target of 

the AFRP for Butte Creek established under CVPIA. Such increases need to be sustainable5 to 

meet CVPIA’s mandate, and the outlook for meeting that mandate is very promising. In Battle 

Creek, a watershed where restoration efforts have been shared by both CALFED and CVPIA, 

the fall-run Chinook salmon natural production has increased to 232 percent of twice its 

average 1967-1991 production. In Clear Creek, the Chinook salmon natural production has 

 

5 Sustainable doubling of natural production is the CVPIA goal for the AFRP effort and a statistical 

process is being developed to assist in that determination. 
CVPIA – Annual Report for Fiscal Year 2004 52 

increased to 172 percent of twice its average 1967-1991 production. Three other Chinook 

salmon populations appear very close to their numeric targets--American River fall-run, 

Mokelumne River fall-run, and Battle Creek late fall-run. 

Actions taken under the CVPIA and other restoration programs such as CALFED are believed 

to have greatly influenced the significant resurgence in anadromous fish populations in widely 

dispersed areas of the Central Valley. They involve several different types of activities, 

including the removal of smaller old dams and barriers reopening many miles of spawning 

habitat, carefully planned deposition of gravel recreating lost spawning habitat, improvement 

of stream-side habitat, better management of available instream water supplies, addition of fish 

screens at many intakes protecting both seaward-migrating smolt and adults returning to 

spawn, support for larger habitat restoration efforts in the watershed, and surveys and research 

work to help fishery biologists better understand workings of the Central Valley fishery and 

ways to re-invigorate its fish populations. 

Spawning gravel replenishment has developed as an essential and highly effective tool to 

improve anadromous fish populations on many streams. Nearly 11,000 tons of gravel was 

placed in the Upper Sacramento and the Stanislaus rivers in 2004. Salmon use the new gravel 

beds to spawn, helping increase fish numbers in those streams. In some streams, deeper pools 

that shelter salmon predator fish have been re-configured to eliminate the threat to anadromous 

fry. 

To be sure, there is much more work to be accomplished. Challenges are particularly complex 

on rivers where the largest, most important dams prevent migration to historic headwater 

habitats. Even so, some improvements appear significant, including near-achievement of the 

numeric AFRP target for fall-run Chinook salmon on the American and Mokelumne rivers, 77 

percent of the numeric target for fall-run on the Feather River, and 67 percent for fall-run on the 

Yuba River. The program continues to make progress on other smaller streams. 

Important achievements were also made as a result of the refuge water supply program, 

keystone in efforts to reinvigorate and expand other imperiled bird, fish and animal 

populations in the Central Valley. In 2004, the CVPIA acquired and/or conveyed nearly 71,000 

acre feet of Level 4 water, historically needed but not widely available for refuges in the past, 

and provided 100 percent of the more reliable Level 2 refuge water supplies. The increased 

water availability expanded refuge wetland habitat by thousands of acres and kept water 

available to birds for longer periods. Bird numbers continue to reflect the improved conditions. 

 

Overall, nearly 65,000 acre feet of Level 4 refuge water supplies was acquired in 2004 from 

willing sellers, at a cost of about $100 per acre-foot. The direct result of these acquisitions 

continues to be a much larger, healthier bird population. Kern National Wildlife Refuge 

(NWR), for example, had 50 white-faced ibis the year before CVPIA and counted 8,000 in 2004. 

Sutter NWR counted 100 ibis in 1991 and a staggering 15,000 in 2004. Another bird species 

showing renewed vigor is the tri-colored blackbird, a species not yet listed but which has been 

identified by some environmental interests as needing protection. It had an identified 

population of 75,000 birds at Delevan NWR in 2004. 
CVPIA – Annual Report for Fiscal Year 2004 53 

Other types of habitat restoration also achieved significant progress in 2004. The Habitat 

Conservation Program participated in the acquisition and/or restoration of nearly 7,000 acres of 

important Central Valley habitat. Restoration included areas along the Sacramento River in 

Tehama County, at Drumheller Slough in Glenn County and at several sites in Santa Clara 

County. Additionally, habitat was acquired along a San Joaquin River tributary in Madera 

County and in the Carizzo Plain in Kern County. 

To Continue Progress in the Future

Although some of the modifications made to Central Valley water system structures and its 

habitats will provide long-term benefit for species, continued progress will require a solid level 

of support in the coming years. Limited and fluctuating budgets may make it difficult to meet 

the immediate needs or to sustain efforts without large infusions of funds from other sources. 

The Anadromous Fish Screen Program, for example, has a current backlog of active projects 

requiring approximately $40 million in additional program funds to complete, yet the FY 2005 

budget provides only 20 percent of that amount ($8.2 million). Similarly, the Water Acquisition 

Program struggles to provide sufficient additional water to meet fish and wildlife needs. At 

current prices, provision of full Level 4 refuge water supplies (159,000 af) will require more than 

$19 million annually to achieve, yet the FY 2005 budget provides less than half that amount. 

The 12-year commitment to the San Joaquin River Agreement (SJRA), which provides pulse 

flows to the lower San Joaquin River and anadromous fish attraction flows in certain San 

Joaquin River tributaries, costs roughly $6.9 to $9.7 million annually (depending on the 

hydrologic year type), accounting for as much as 67 percent of the total FY 2005 Water 

Acquisition Program budget of $12.6 million. As a result, very little funding will be available to 

acquire water for instream flows on other Central Valley streams during the life of the current 

SJRA agreement, scheduled to expire after FY 2011. Other essential CVPIA programs, most 

notably the AFRP, continues to be under-funded resulting overall in a program whose 

implementation is much slower than expected. 

 

Interior is proud of its efforts to date, but recognizes the job is far from being complete. The 

Department believes implementation of the CVPIA is on the right course, a course that will 

continue to provide increasingly significant benefits if support remains steady.