Implementation of the 

Central Valley Project Improvement Act 

Annual Report for Fiscal Year 2006 

U.S. Department of the Interior 

Fish and Wildlife Service 

Bureau of Reclamation 

January 2008
CVPIA – Annual Report for Fiscal Year 2006 2 

Contents 

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

IMPLEMENTING THE CVPIA....................................................................................................... 5

Coordination.................................................................................................................................. 9

Funding Sources.......................................................................................................................... 10

FISCAL YEAR 2006ACCOMPLISHMENTS AND RESTORATION FUND DOLLARS 

OBLIGATED ....................................................................................................................... 14

Project Title: Anadromous Fish Restoration Program........................................................ 14

Project Title: Evaluation of Anadromous Fish Instream Flow Needs .............................. 25 

Project Title: Habitat Restoration Program .......................................................................... 27

Project Title: Management of Dedicated CVP Water for Environmental Purposes....... 29

Project Title: Water Acquisition Program............................................................................. 32

Project Title: Tracy Pumping Plant Mitigation Program.................................................... 35

Project Title: Contra Costa Canal Pumping Plant Fish Screen Project ............................. 37

Project Title: Flow Fluctuation/Reservoir Storage Management Program..................... 38

Project Title: Red Bluff Diversion Dam Fish Passage Program......................................... 38

Project Title: Coleman National Fish Hatchery ................................................................... 39 

Project Title: Clear Creek Restoration Program................................................................... 40

Project Title: Spawning Gravel Replenishment Program................................................... 41

Project Title: Comprehensive Assessment and Monitoring Program .............................. 44

Project Title: Anadromous Fish Screen Program ................................................................ 45

Project Title: Trinity River Restoration Program................................................................. 47 

Project Title: San Joaquin River Comprehensive Plan........................................................ 49

Project Title: Refuge Water Supply Program – Water Conveyance Component............ 51

Project Title: Refuge Water Supply Program – Facilities Construction Component...... 54

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

Component ........................................................................................................ 54

Project Title: Ecosystem/Water System Operations Models............................................. 55

Project Title: Land Retirement Program ............................................................................... 57

DISCUSSION OF CVPIA IMPLEMENTATION AND RESULTS......................................... 59 

Anadromous Fish - Biological Response ..................................................................................... 60

Refuges and Waterfowl – Biological Response....................................................................... 62

Other Fish and Wildlife – Accomplishments.......................................................................... 63

CONCLUSIONS ....................................................................................................................... 64 

Quantifiable Progress in 2006.................................................................................................... 64 

To Continue Progress in the Future ......................................................................................... 66 

REFERENCES ....................................................................................................................... 66
CVPIA – Annual Report for Fiscal Year 2006 3 

FIGURES 

1 CVPIA Expenditures by Fund Source – Fiscal Year 2006..................................................... 12 

2 CVPIA Expenditures by Fund Source – Fiscal Years 1993-2006.......................................... 12 

3 Total CVPIA Expenditures by Action Category – Fiscal Year 2006 .................................... 13 

4 Total CVPIA Expenditures by Action Category – Fiscal Years 1993-2006 ......................... 13 

TABLES 

1 Numbers and percentages of Central Valley watersheds in which AFRP limiting 

factors have been addressed with AFRP funding, and AFRP Objectives (1-6) that 

were supported by the projects, since 1995 ........................................................................... 16 

2 Percent of AFRP watershed limiting factors addressed and AFRP projects 

implemented, related to Chinook salmon production during the 1967-1991 and 

1992-2006 periods ....................................................................................................................... 18 

3 Adult Salmonid Escapement Trends on CVP-Controlled Streams (anadromous fish 

doubling goal)............................................................................................................................. 31 

4 Summary of water purchases and executed agreements for the Water Acquisition 

Program in FY 2006 .................................................................................................................. 32 
CVPIA – Annual Report for Fiscal Year 2006 4 

Central Valley Project Improvement Act 

Annual Report for Fiscal Year 2006 

INTRODUCTION

The Central Valley Project (CVP) is one of the world’s largest water storage and 

conveyance systems, comprising 20 dams and reservoirs (capable of storing 9 million 

acre-feet of water), 11 powerplants, 500 miles of major canals and aqueducts, 3 fish 

hatcheries, and numerous related facilities such as pumping plants and power lines. 

Annually, the CVP conveys about seven-million acre-feet (AF) of water, primarily from 

northern California southward, from the Sacramento, Trinity, American, Stanislaus, and 

San Joaquin Rivers to agricultural and municipal water users and wildlife refuges in the 

Sacramento and San Joaquin Valleys and the San Francisco Bay Area. For almost 70 

years, California has depended on the CVP for meeting a large part of its water needs. 

Due to the way that water is captured, moved, and co-mingled with other water 

supplies such as those of the State Water Project (SWP), the CVP affects sensitive 

ecosystems of the Central Valley, Delta estuary, San Francisco Bay, and Trinity River, 

particularly in drought years. Many complex, and often unresolved, water issues 

revolve around finding an economically viable balance between an increasing urban and 

agricultural demand for water and the health and well-being of California’s river and 

Delta estuary ecosystems. 

On October 30, 1992, Title 34 of Public Law 102-575, the Central Valley Project 

Improvement Act (CVPIA), was signed into law by the President. This landmark piece 

of legislation mandates changes in the purposes and management of the Bureau of 

Reclamation’s (Reclamation) Central Valley Project (CVP). The legislation specifically 

directed the Secretary of the Department of the Interior (Interior) “to protect, restore, 

and enhance fish, wildlife, and associated habitats in the Central Valley and Trinity 

River basins of California” while also achieving “a reasonable balance among competing 

demands for use of the Central Valley Project water...” 

Reclamation and the U.S. Fish and Wildlife Service (Service) have primary responsibility 

for implementing CVPIA’s many provisions. Reclamation has the primary 

responsibility for all budget submissions supporting both agencies including all 

associated duties for appropriations, finance and accounting from an overall 

perspective. Reclamation also has responsibility for engineering, CVP operations, 

design, and construction of specific project features. The Service has primary 

responsibility for decisions on biological resource issues, studies on fish and wildlife 

populations and their habitat requirements, fishery restoration program direction, and 

for the planning, design, and decisions on the administration of fish and wildlife 

facilities. 
CVPIA – Annual Report for Fiscal Year 2006 5 

This report is a summary of the actions taken by Reclamation and the Service, working 

with other Federal agencies, the State of California (State), and numerous partners and 

stakeholders during fiscal year (FY) 2006. 

IMPLEMENTING THE CVPIA 

The purposes of the CVPIA are provided in Section 3402 of the Act. To achieve these 

purposes, a large number of provisions were incorporated into the statute. The 

provisions include, but are not limited to, 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. The provisions also provide for 

system-wide modeling, numerous investigations and studies, and monitoring to assess 

the biological results and effectiveness of CVPIA actions. To help implement these 

measures, section 3407 of the Act established a Restoration Fund from sources and 

revenues provided for under other sections of the Act. 

Any action undertaken to implement the CVPIA is designed to the maximum extent 

practicable to contribute to the attainment of CVPIA goals. Several factors are 

considered in establishing priorities for CVPIA actions including, the importance of the 

action in achieving CVPIA program goals, biological benefits, geographic area, amount 

of planning needed to implement the action, technical feasibility, cost effectiveness, and 

the availability of partners and funding. Actions proposed for implementation under 

the CVPIA are prioritized on an annual basis with stakeholder and public involvement. 

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

developing and implementing three main programs for fish and wildlife restoration, as 

identified in the provisions of the Act. The most ambitious of these three programs is 

the Anadromous Fish Restoration Program (AFRP). The second program for fish and 

wildlife restoration was to supply “firm water supplies of suitable quality to maintain 

and improve wetland habitat areas” on Federal and State refuges and other migratory 

waterfowl habitats in the Central Valley. The third was “to address other identified 

adverse environmental impacts of the Central Valley Project...” – impacts not 

specifically enumerated in other provisions of the Act. 
6

The Anadromous Fish Restoration Program

Section 3406(b)(1) of the Act states “... implement a program which makes all reasonable 

efforts to ensure that, by the year 2002, natural production of anadromous fish in Central 

Valley Rivers and streams will be sustainable, on a long-term basis, at levels not less 

than twice the average levels attained during the period of 1967-1991...” The process to 

identify reasonable actions for anadromous fish restoration was vetted in a public forum 

with stakeholders, partners, and other interested parties and was eventually described 

in the Final Restoration Plan for the Anadromous Fish Restoration Program (AFRP) (USFWS 

2001) (AFRP Restoration Plan). Many of the other measures and programs in Section 

3406 were intended to contribute to the effort of doubling anadromous fish. 

The Delta has been one of the highest priority geographic areas for anadromous fish. All 

species and races of anadromous fish must pass through the Delta, both as in-migrating 

adults moving upstream and as out-migrating juveniles moving to the ocean. The 

opportunity for implementing measures in the Delta with widespread beneficial effects 

for all anadromous fish is tremendous. Emphasis has been on providing adequate flows 

to improve migration and reproductive success and 

on reducing water diversions during peak periods 

when out-migrating juvenile anadromous 

salmonids and 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 are 

also being employed as part of normal operations of 

the CVP. 

The east-side tributaries of the Sacramento River are 

another major focus area for anadromous fish. 

These streams support the last significant runs of 

the threatened spring-run Chinook salmon. Once 

the most numerous race in the valley, the springrun 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 in-stream flow, laddering or removal of 

dams and other impediments to migration, 

screening or removal of water diversion 

infrastructure, maintenance of spawning habitat, 

and acquisition and restoration of riparian habitats 

that shade the stream channel from solar heating 

and provide woody debris and nutrients to the aquatic ecosystem. 
7

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

Creek, and the Yuba River, also have 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 water during the summer. 

Restoration efforts on these streams have focused on the same types of measures as for 

the spring-run Chinook salmon. 

The Refuge Water Supply Program 

With the decline of natural 

wetlands in the Central Valley, 

wildlife specialists have been 

forced to intensively manage the 

remaining 300-400 thousand acres 

of wetlands to accommodate the 

millions of wintering waterfowl, 

shorebirds, and other wildlife that 

depend on wetlands for their 

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 tradeoffs of one species for another has 

been 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 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, 

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 
8

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 crops 

leaving waste grain, primarily in the Sacramento Valley. Unfortunately, this program, 

with its conjunctive use of lands for agriculture and waterfowl, has expired. 
9

The (b)(1) “Other: Habitat Restoration Program 

The CVPIA directs us to make all reasonable efforts to address the environmental 

impacts of the CVP that are not specifically dealt with in 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 

species listed as threatened or endangered that are not addressed in other provisions of 

the CVPIA, some of which are on the verge of extinction. Emphasis has 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-3408(h) 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 Bay-Delta Program’s 

(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 this purpose. 
10

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 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 creditable 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 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 

14 years (1993–2006) has cost approximately $831.2 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), GlennColusa Irrigation District Fish Screen Project ($43 million), rehabilitation of Coleman 

National Fish Hatchery ($22 million), and fixing the fish passage problems at Red Bluff 

Diversion Dam (RBDD) ($42 million) and Tracy and Contra Costa Canal Pumping plants 

($22 million). Other efforts, however, such as the 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 $831.2 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 2006, $54.6 million was appropriated in the Restoration Fund for the various 

CVPIA programs and actions. 
11

Since its inception more than nine 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 show the obligations by fund source; Figure 1 for FY 2006 and Figure 2 

for the 14-year period since FY 1993. 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 to habitat restoration measures for anadromous 

fish, measures believed necessary to help achieve our anadromous fish doubling goal, 

and on acquiring and providing water for refuges. Figures 3 and 4, respectively, show 

the total distribution of these obligations among action categories for FY 2006 and the 

entire FY 1993-2006 period. 
12

FIGURE 2

CVPIA OBLIGATIONS BY FUND SOURCE

Fiscal Years 1993-2006

59%

33%

3%

5% 0%

Restoration Fund $485.5 million

Water & Related Resources $275.4 million

State Past Cost Share $24.5 million

State Current Cost Share $44.8 million

Donation $1 million

FIGURE 1

CVPIA OBLIGATIONS BY FUND SOURCE

Fiscal Year 2006

75%

22%

 3% 0%

Restoration Fund $54.6 million

Water & Related Resources $16 million

State Past Cost Share $.02 million

State Current Cost Share $1.8 million
13

FIGURE 3

CVPIA OBLIGATIONS BY ACTION CATEGORY

Fiscal Year 2006

36%

23%

2%

35%

0% 4%

Anad. Fish - Habitat Restoration $25.3

million

Anad. Fish - Structures $17 million

Studies/Investigations/Modeling $1.4 million

Refuges & Waterfowl $25.5 million

Monitoring $0.20 million

Other Fish and Wildlife $3 million

FIGURE 4

 TOTAL CVPIA OBLIGATIONS BY ACTION CATEGORY

 Fiscal Years 1993-2006

4%

8%

23%

37%

24%

3%1%

Admin./Contracts/Improved Water Mgmt.

$30.0 million

Other Fish and Wildlife $69.5 million

Anad. Fish - Habitat Restoration $192.1

million

Anad. Fish - Structures $306.3 million

Refuges & Waterfowl $201.3 million

Studies/Investigations/Modeling $22.6

million

Monitoring $9.4 million
14

FISCAL YEAR 2006 ACCOMPLISHMENTS AND RESTORATION FUND 

DOLLARS OBLIGATED 

Since passage of the CVPIA, Reclamation and the Service, with assistance of the State 

and the cooperation of many partners, have completed many of the provisions of the 

Act, including 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 2006.

Project Title: Anadromous Fish Restoration Program

 CVPIA Section 3406(b)(1) 

FY 2006 Funding: $ 3,722,303 

FY 2006 Accomplishments (AFRP Program Overview): 

Passage of the CVPIA led to establishment of the Anadromous Fish Restoration Program 

(AFRP) and directed Interior to include all reasonable efforts to at least double the 

natural production, on a sustainable long-term basis, of six species of anadromous fish 

in Central Valley rivers and streams over levels that existed during the 1967-1991 period. 

Anadromous fish are those species that are born in freshwater but migrate to the ocean 

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 or runs), steelhead, striped bass, American shad, white 

sturgeon, and green sturgeon. 

All actions to achieve the anadromous fish doubling goal were guided by the Final 

Restoration Plan developed by AFRP staff in coordination with experts from many 

agencies and stakeholder groups. The Final Restoration Plan, released in 2001 after 

extensive input and public review, identified six general objectives necessary to achieve 

the anadromous fish 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; 
15

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

and 

6. Involve partners in the implementation and evaluation of restoration actions. 

The Final Restoration Plan was completed in 2001 to guide the long-term development 

of the AFRP. The Final Restoration Plan provides a programmatic-level description of 

the AFRP and, is used to guide the implementation of all of the provisions of the CVPIA 

that contribute to the goal of making all reasonable efforts to at least double natural 

production of anadromous fish (AFRP doubling-goal). The following provisions 

contribute to accomplishing the goal of the AFRP (b)(1) program: b1B, b2, b3, b12, b13, 

b16, and b21. The Final Restoration Plan presents a list of reasonable actions and 

evaluations and a process by which actions and evaluations were determined to be 

reasonable. The Restoration Plan identifies the need for partners, local involvement, 

public support, adaptive management, and flexibility as key attributes of the AFRP 

approach. 

To implement this plan, in 1995 the USFWS established federal Habitat Restoration 

Coordinator (HRC) positions assigned to specific geographic areas from the upper 

Sacramento River and its major tributaries south to the San Joaquin River and its major 

tributaries. In 1998, the AFRP added three more HRCs from the California Department 

of Fish and Game (DFG) to this effort. These state HRCs provide assistance to the 

USFWS and ensure close coordination with the DFG the state agency with trust 

authority for managing anadromous fish populations in California. In their assigned 

areas, HRCs represent the AFRP, develop and nurture partnerships, develop projects 

with partners that contribute to the AFRP doubling-goal, and oversee all aspects of 

implementation of projects in which the AFRP invests funds. Together, the USFWS and 

DFG HRCs form an interagency team to coordinate, develop and implement restoration 

projects consistent with the goal, objectives, strategies, processes and priorities described 

in the Restoration Plan. 

The AFRP is one of five Central Valley Project Improvement Act (CVPIA) programs that 

has been integrated with the California Bay-Delta Authority (CBDA) Ecosystem 

Restoration Program (ERP) (Record of Decision, 2000). To facilitate this integration, the 

above objectives are included in the CBDA ERP Draft Stage 1 Implementation Plan. 

These objectives are also complementary to other goals and objectives listed in the Draft 

Stage 1 Implementation Plan and would help address the objectives of the CBDA’s 

Multi-Species Conservation Strategy and the Biological Opinion for the CVPIA. The 

AFRP shares CBDA’s vision of the Single Blueprint concept which provides a unified 

and cooperative approach to restoration. The AFRP is committed to integrating its 

activities with the Ecosystem Restoration Program’s actions and evaluations and using a 

scientifically-based adaptive management approach to achieve AFRP objectives.

 

Summary of AFRP Biological Benefits Since 1995 

Environmental limiting factors
16

AFRP projects implemented since 1995 have addressed eight major categories of limiting 

factors, as identified in AFRP’s Working Paper on Restoration Needs, Habitat Restoration 

Actions to Double Natural Production of Anadromous Fish in the Central Valley of California 

(AFRP Working Paper) (USFWS 1995a). The projects were defined in the Final 

Restoration Plan as reasonable (USFWS 2001:11-12) restoration actions and evaluations 

necessary to address limiting factors associated with anadromous fish restoration in 

Central Valley watersheds. 

Table 1 shows the eight major categories of limiting factors, numbers and percentages of 

Central Valley watersheds where actions were taken, and which AFRP objectives were 

addressed. Insufficient flow (Objective 1) is a limiting factor category associated with all 

Central Valley watersheds (26 CVPIA identified watersheds) (USFWS 2001) and has 

been partially addressed in about 41 percent of the watersheds. Adult and juvenile 

salmon and steelhead entrainment and passage, and stream habitat restoration are also 

important limiting factor categories, and were partially addressed in at least 22 percent 

of the Central Valley watersheds. Measures that addressed the adult and juvenile 

entrainment limiting factor category are helping to meet Objective 2. All measures that 

addressed the fish passage limiting factor category are helping to meet Objective 3. 

Measures that evaluate or improve survival, assess effects of hatchery fish on natural 

production, and involve partners in watershed planning are helping meet Objectives 4-6. 

Table 1. Numbers and percentages of Central Valley watersheds in which AFRP 

limiting factors have been addressed with AFRP funding, and AFRP Objectives (1-6) 

that were supported by the projects, since 1995.a

AFRP limiting factor 

categories 

Number (and percent) of 

watersheds where actions 

were taken 

AFRP objectives addressed 

(1-6) 

Insufficient flow 11 (41) 1 

Adult and juvenile 

entrainment 7 (26) 2 

Stream habitat 

restoration 6 (22) 1 

Fish passage 6 (22) 3 

Predation 4 (15) 4 

Spawning habitat 4 (15) 1 

Effects of hatchery 

fish on natural stocks 3 (11) 5 

Erosion and 

sediment control 2 (7) 1 
CVPIA – Annual Report for Fiscal Year 2006 17 

Overall progress toward salmon production goals in Central Valley watersheds

Progress toward addressing environmental limiting factors identified in the AFRP 

Working Paper and implementation of restoration actions in the Final Restoration Plan 

are summarized in Table 2. About 34 percent of all limiting factors identified in the 

AFRP Working Paper were addressed, and about 27 percent of the Final Restoration 

Plan actions and evaluations were implemented during 1995-2005. Several restoration 

actions will continue in perpetuity and must be renewed seasonally (e.g., instream flows 

and spawning gravel), due to such things as geomorphological impediments, including 

high dams that intercept natural gravel recruitment. 

 

The total estimated natural production of Central Valley Chinook salmon increased 

about 5 percent from the 1967-1991 baseline period (Table 2), well below the doubling 

goal established by CVPIA. Central Valley streams where most environmental limiting 

factors have been improved and restoration actions implemented, salmon production 

has increased about two, or more, times beyond the CVPIA doubling goal (e.g., Butte 

and Clear creeks). Uncertainty remains, however, whether this short-term increase is 

sustainable in either creek. 
CVPIA – Annual Report for Fiscal Year 2006 18 

Table 2. Percent of AFRP watershed limiting factors addressed and AFRP projects implemented, related to Ch

production during the 1967-1991 and 1992-2005 periods. 

AFRP Central 

Valley Watersheds 

Percent 

Limiting 

Factors 

Addressed (a) 

Percent AFRP 

Projects 

Implemented 

(b) 

Salmon 

Natural 

Production 

Doubling Goal 

(c,d)

1967-1991 

Average 

Natural 

Salmon 

Production (e) 

1992-2005 

Average 

Natural 

Salmon 

Production (e)

All AFRP Central Valley watersheds, fall-, late-fall-, spring-, winter-run (g)

990,000 497,241 514,12

All AFRP Central Valley watersheds, fall -run (g)

750,000 374,217 469,87

All AFRP Central Valley watersheds, late-fall -run (g)

68,000 34,182 20,05

All AFRP Central Valley watersheds, spring -run (g)

68,000 34,425 16,90

All AFRP Central Valley watersheds, winter-run (g)

34 27 

110,000 54,417 7,29
CVPIA – Annual Report for Fiscal Year 2006 19 

AFRP Central 

Valley Watersheds 

Percent 

Limiting 

Factors 

Addressed (a) 

Percent AFRP 

Projects 

Implemented 

(b) 

Salmon Natural 

Production 

Doubling Goal 

(c,d)

1967-1991 

Average 

Natural Salmon 

Production (e) 

1992-2005 

Average 

Natural Salmon 

Production (

Upper Mainstem Sacramento River and Tributaries Upper mainstem Sacramento River, fall-run 

230,000 115,338 95,1

Upper mainstem Sacramento River, late-fall-run 

69,000 33,931 20,8

Upper mainstem Sacramento River, spring-run 

59,000 29,402 1,0

Upper mainstem Sacramento River, winter-run 

67 41 

110,000 54,294 7,2

Clear Creek, fallrun 100 100 7,100 3,574 12,5
CVPIA – Annual Report for Fiscal Year 2006 20 

AFRP Central 

Valley Watersheds 

Percent 

Limiting 

Factors 

Addressed (a) 

Percent AFRP 

Projects 

Implemented 

(b) 

Salmon 

Natural 

Production 

Doubling Goal 

(c,d)

1967-1991 

Average 

Natural 

Salmon 

Production (e) 

1992-2005 

Average 

Natural 

Salmon 

Production (e)

Battle Creek, fallrun (g) 10,000 5,012 22,82Battle Creek, latefall-run (g)

40 25 

550 273 66

Antelope Creek, fall-run 100 100 720 361Bear Creek included in Miscellaneous small tributaries, fall-run 

0 0 Data n.a. Data n.a. Data n.a

Paynes Creek, fallrun 0 0 330 170 Data n.aStoney Creek, fallrun 0 0 Not set Data n.a. Data n.a
CVPIA – Annual Report for Fiscal Year 2006 21 

AFRP Central 

Valley Watersheds 

Percent 

Limiting 

Factors 

Addressed (a) 

Percent AFRP 

Projects 

Implemented 

(b) 

Salmon 

Natural 

Production 

Doubling Goal 

(c,d)

1967-1991 

Average 

Natural 

Salmon 

Production (e) 

1992-2005 

Average 

Natural 

Salmon 

Production (e)

Cottonwood Creek, fall-run 0 0 5,900 2,962 3,58Thomes Creek, fallrun 0 0 Not set Data n.a. Data n.aElder Creek, fallrun 0 0 Not set Data n.a. Data n.aMiscellaneous small tributaries, fall-run (h) 0 100 

1,100 550 Data n.a

Lower Sacramento River and Delta Tributaries Feather River, fallrun (g) 0 0 170,000 86,007 113,85Yuba River, fall-run 43 36 66,000 33,254 40,97Bear River, fall-run 0 0 450 636 Data n.aAmerican River, fall-run (g) 29 15 160,000 80,846 144,83Cosumnes River, fall-run 50 33 3,300 1,659 62
CVPIA – Annual Report for Fiscal Year 2006 22 

AFRP Central 

Valley Watersheds 

Percent 

Limiting 

Factors 

Addressed (a) 

Percent AFRP 

Projects 

Implemented 

(b) 

Salmon Natural 

Production 

Doubling Goal 

(c,d)

1967-1991 

Average 

Natural Salmon 

Production (e) 

1992-2005 

Average 

Natural Salmon 

Production (

Mokelumne River, fall-run (g) 42 23 9,300 4,679 9,8Calaveras River, winter-run 40 33 2,200 770San Joaquin River and Tributaries San Joaquin River, fall-run (i) 10 15 Not set 38,818 25,2Stanislaus River, fall-run 60 33 22,000 10,868 6,7Tuolumne River, fall-run 55 40 38,000 18,946 9,5Merced River, fallrun (g) 58 38 18,000 9,004 8,9

a Limiting factors identified in USFWS (1995). This column includes limiting factors partially addressed; does not consi

of actions or limiting factors. 

b Projects identified in USFWS (2001). Percentages represent restoration actions implemented and does not imply that a

limiting factors are completed; e.g., actions such as replenishing gravel or restoring riparian habitat are general in nat

AFRP Restoration Plan, these types of actions must be repeated in perpetuity (gravel replenishment) for that wat

different sections of the watershed (riparian restoration). 

c Chinook salmon doubling goals from USFWS (2001). d Targets for each of the races of Chinook salmon may not add up to the target for all races combined due to rounding. 
CVPIA – Annual Report for Fiscal Year 2006 23 

e Escapement numbers used for calculating natural production estimates for 1967-1991 are from Mills and Fisher (1994) a

California Department of Fish and Game, Grand Tab (CDFG - 2007). May vary from half the USFWS, 2001, numeric gorecalculations and corrections. Methods to calculate natural production from USFWS (1995a:2-IX-5-18). 

f Percent change in natural production calculated by subtracting natural production for 1967-1991 from natural productio

dividing by natural production for 1967-1991. 

g Hatchery supported Chinook salmon production. 

h Miscellaneous streams include production estimates of fall-run Chinook salmon in Spring Gulch, China Gulch, Olney, 

 and Bear creeks above RBDD. i San Joaquin River is the sum of the Stanislaus, Tuolumne, and Merced rivers. 
CVPIA – Annual Report for Fiscal Year 2006 24 

FY 2006 Funded Projects 

During FY 2006, the AFRP was limited to funding mostly ongoing projects due to a limited 

budget. 

Accomplishments for FY 2006 in the Sacramento Basin

The upper Sacramento Basin tributaries where accomplishments occurred in FY 2006 include 

Cow, Mill, Deer, Cottonwood, Battle, Bear, Antelope, and Big Chico creeks Accomplishments 

included developing restoration projects with partners, oversaw implementation of AFRP 

funded projects, and represented the goals of the Anadromous Fish Restoration Program. 

Worked with local landowners of the Cow, Mill, Deer, Cottonwood, Battle, Bear, Antelope, and 

Big Chico watershed groups, to develop restoration projects and provided technical expertise. 

The replacement of the fish bypass pipe at the Orwick Diversion site was completed (AFRP 

Action 4 - Fish passage at Orwick Diversion). 

The lower Sacramento Basin tributaries where accomplishments occurred in FY 2006 include 

Big Chico and Butte Creek, and the Yuba River. On Big Chico Creek funds were provided to 

complete the permitting and environmental documentation required to begin the construction 

of Iron Canyon Fish Ladder. Funds were also provided to support efforts to identify, apply for, 

and acquire the funds to complete the construction of the ladder including final engineering 

design and cost estimates. For the White Mallard Dam and fish ladder Phase III construction on 

Butte Creek, management, on-site management/facilitation, engineering, environmental 

assistance, construction and post construction monitoring were provided. Also, preliminary 

engineering and environmental assessment for the Five Points/Behring Ranch Diversion Canal 

were provided. A salmon life history study was completed for both Butte and Big Chico Creek. 

Yuba River accomplishments included characterizing the fluvial geomorphology, sediment 

transport dynamics, and in-stream hydraulics of key spawning reaches to build a predictive 

model for adult spawning locations. Gravel movement was monitored with tracer rocks and 

redd surveys for a pilot gravel injection for spring-run Chinook directly below Engelbright 

Dam. Data was collected from fish passage events to better understand the timing, abundance, 

population trends, and response to changing flow and temperature conditions of adult spring 

and fall- run Chinook salmon, and Central Valley steelhead in the Lower Yuba River. This 

information will help improve management of these species in the Lower Yuba River, including 

actions such as salmonid habitat restoration projects and providing appropriate in-stream flow 

regimes. Activities included synthesizing collected information to improve management of 

these species through actions such as aquatic habitat restoration projects and regulating instream flow regimes. The project will be closed this year. 

Accomplishments for FY 2006 in the San Joaquin Basin

The San Joaquin Basin tributaries where accomplishments occurred in FY 2006 include the 

Cosumnes, Calaveras, Mokelumne, Stanislaus, and Merced rivers. For the Cosumnes River 

Passage and Habitat Improvement Project, permitting and final phases of project planning was 

completed as well as extraction of gravel to be used and stored on-site in preparation of gravel 

placement. For the Calaveras River Salmonid Life History Limiting Factor Analysis, data was 

collected on steelhead and fall-run Chinook salmon passage and stranding. The data collected 

will be used to manage flows and assist in prioritization and evaluation of structural repairs. 

On the Mokelumne River, second year funding was used to complete the analysis of fall-run 

Chinook salmon otoliths to determine the ratio of hatchery to wild fish. Data will be used to 
CVPIA – Annual Report for Fiscal Year 2006 25 

update the production calculations which the AFRP program goals are based. Funds were also 

provided to purchase spawning gravel materials used for an ongoing project to increase 

spawning gravel quantity and improve gravel quality at known spawning sites for fall-run 

Chinook salmon and steelhead downstream of Camanche Dam. The initial microstructure and 

microchemistry analysis for the first 100 otolith samples for an evaluation of Mokelumne River 

Chinook salmon of hatchery and natural origin was completed. Stanislaus River 

accomplishments included the collection of data, initiation of an additional pilot project to 

coded-wire tag emigrating juvenile salmonids, construction of a trailer, efficiency tests and 

passage estimates for the year, and an evaluation of environmental variables effecting fish 

passage for a juvenile Chinook salmon rotary screw trap monitoring and outmigration study. 

Other completions included conceptual models for each race of Chinook and steelhead, and a 

summary table highlighting top priorities for anadromous fish restoration on the Stanislaus 

River. Also, progress was made towards completing a decision support system to provide 

capacity for identifying the effects of identified restoration activities. The Merced River screw 

trap was operated and collected data January 23rd to June 1st. Efficiency tests were conducted 

and passage estimates were made. Progress was also made towards a report on the natural and 

hatchery juvenile Chinook salmon movement. 

Another accomplishment was the test and demonstration of a portable Alaskan weir to count 

and characterize runs of anadromous fish where data was collected over a period of time to 

measure spring-run Chinook salmon escapement. The data was summarized and an annual 

report was produced. This work is being done for a five year comprehensive report. 

Project Title: Evaluation of Anadromous Fish Instream Flow Needs

 CVPIA Sections 3406(b)(1) and 3406(b)(1)(B) 

FY 2006 Funding: $544,125 

FY 2006 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. 

Biological benefits of activities since 1992 include identifying flow-habitat relationships for 

anadromous salmonids in the following: Merced, American, and Sacramento rivers, and Butte 

Creek. Notably in 2004 to 2006, the flow-habitat relationship for spring-run Chinook salmon 

spawning in Butte Creek was used to increase the spawning flows in the bypass reach of Butte 

Creek, resulting in reduced redd superposition and greater survival of eggs and larvae. 

Monitoring of these results includes screw-trapping in Butte Creek. Also, in 2005, the results of 
CVPIA – Annual Report for Fiscal Year 2006 26 

our flow-habitat relationships for the American River were used to develop a new flow regime 

for the American River, which will result in improved conditions for anadromous salmonids. 

FY 2006 accomplishments were documented (http://www.fws.gov/sacramento/) 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 seven tasks. Task 1 addressed 

Chinook salmon and steelhead rearing in Clear Creek; Tasks 2 and 3 addressed Chinook salmon 

and steelhead spawning and rearing in Clear Creek; Task 4 addressed Chinook salmon and 

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

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

River and Clear Creek, and Chinook salmon and steelhead redd dewatering and juvenile 

stranding in the Sacramento River between Keswick Dam and Battle Creek. 

1. Habitat Suitability Criteria (HSC) Development - Started collection of Clear Creek 

rearing HSC data for fry and juvenile spring run Chinook salmon and 

steelhead/rainbow trout. Clear Creek rearing HSC data collection is 50 percent 

complete. 

2. Habitat Mapping - Habitat mapping for the lower alluvial segment of Clear Creek will 

be conducted in FY 2008. Habitat mapping is 67 percent complete. 

3. Field Reconnaissance and Study Site Selection - Established five study sites for fall-run 

Chinook salmon and steelhead/rainbow trout spawning in the lower alluvial segment of 

Clear Creek. The above activities are 100 percent complete. 

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

and steelhead/rainbow trout fry and juvenile rearing sites on the Yuba River and Clear 

Creek, and started hydraulic data collection for fall-run Chinook salmon and 

steelhead/rainbow trout spawning sites in the lower alluvial segment of Clear Creek. 

All of the above hydraulic data collection should be completed in early FY 2008. 

Hydraulic data collection is 95 percent complete for Yuba River and Clear Creek rearing, 

and 20 percent complete for Clear Creek spawning in the lower alluvial segment. 

5. Modeling of Spawning and Rearing Habitat in Study Streams – Draft reports were 

completed for modeling of spring and fall-run Chinook salmon and steelhead/rainbow 

trout spawning habitat in the Yuba River and modeling of spring and fall-run Chinook 

salmon and steelhead/rainbow trout spawning habitat in Clear Creek between 

Whiskeytown Dam and Clear Creek Road Bridge in FY 2006. These tasks are 90 percent 

completed. These studies resulted in the establishment of flow-habitat relationships for 

spawning and rearing salmonids. 

6. Peer Review - The reports for macroinvertebrate habitat and for redd dewatering and 

juvenile stranding in the Sacramento River between Keswick Dam and Battle Creek, for 

spring and fall-run Chinook salmon and steelhead/rainbow trout spawning habitat in 

the Yuba River, and for spring and fall-run Chinook salmon and steelhead/rainbow 

trout spawning habitat in Clear Creek between Whiskeytown Dam and Clear Creek 

Road Bridge were peer reviewed in FY 2006. These tasks are 100 percent complete. 
CVPIA – Annual Report for Fiscal Year 2006 27 

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

report was prepared in FY 2006. This activity is 80 percent complete. 

Project Title: Habitat Restoration Program

 CVPIA Section 3406(b)(1) “Other” 

FY 2006 Funding: $1,590,238 

FY 2006 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 Endangered Species Act (ESA) or were non-listed State or Federal species of special concern. 

The program began in FY 1996 and has funded 77 new projects located throughout the Central 

Valley. Almost 99,000 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 serpentine soils and 

associated habitats, vernal pool, aquatic, alkali sink and alkali scrub, foothill chaparral, valleyfoothill hardwood, riparian woodland, and grassland. 

In FY 2006, 12 conservation actions were funded. Two of these actions provided additional 

funding to continue projects that were initiated in previous years: 

 1. Continuation of planning phase for restoration of floodplain and vernal pool 

 habitat on the 1,905-acre Sno-Bird Ranch, owned and managed by the Merced 

 National Wildlife Refuge in Merced County. Species that would benefit include 

 the vernal pool tadpole shrimp, vernal pool fairy shrimp, and Colusa grass. 

 2. Continuation of a study by the University of California, Davis, to complete a 

 characterization of vernal pool vegetation in relation to habitats; documentation 

 of the affiliation of special status species to particular plant communities; and 

 creation of guidelines for the conservation and restoration of vernal pool 

 diversity. Various vernal pool species throughout the Sacramento Valley benefit 

 from this project. 

The 10 new actions for FY 2006 are the following: 

 1. Funds were provided to California State University, Sonoma, to study the 

 reproductive success of five vernal pool plant species located throughout the 

 Sacramento Valley. The study focused on how reproductive success can be 

 improved, which will ultimately help prevent the extinction/decline of these 

 species due to threats from invasive grasses. Species benefited include hairy 

 orcutt grass, Sacramento orcutt grass, Solano grass, Greene’s tuctoria, and Colusa 

 grass. 
CVPIA – Annual Report for Fiscal Year 2006 28 

 2. Funds were provided to Point Reyes Bird Observatory to conduct a study on the 

 least Bell’s vireo in Stanislaus County. The study involved four main tasks: (1) 

 developing a map of suitable least Bell’s vireo habitat; (2) monitoring the 

 presence and abundance of the least Bell’s vireo; (3) monitoring least Bell’s vireo 

 productivity; and (4) assessing brown-headed cowbird impacts in restored areas. 

 3. Funds were provided to Eric Hansen Associates to conduct a study on the 

 potential presence of giant garter snakes north and east of the San Joaquin River, 

 and the current status of declining historical populations south and east of the 

 San Joaquin River in the Grassland Ecological Area in Merced County. A goal of 

 the study was to provide an elementary foundation for long-term monitoring of 

 giant garter snake populations in the San Joaquin Valley. Additionally, tissue 

 samples were provided for a parallel genetic study conducted by Dr. Tag 

 Engstrom, California State University, Chico (see #4). 

4. Funds were provided to Dr. Tag Engstrom, California State University, Chico, to 

 conduct a study that explored the genealogical relationships of giant garter snake 

 populations across the range of the species and, if appropriate, delineate 

 genetically, based on distinct population segments. 

 

 5. Funds were provided to the Tulare Basin Wildlife Partners to write the Southern 

 San Joaquin Valley Conceptual Area Protection Plan (CAPP), for the Tulare Lake 

 - Sand Ridge Project Unit (CAPP Unit 2), and the Buena Vista Lake Project Unit 

 (CAPP Unit 3) for Tulare County. Species benefited include vernal pool fairy 

 shrimp, blunt-nosed leopard lizard, Tipton kangaroo rat, and San Joaquin kit fox. 

 6. Funds were provided to the Sequoia Riverlands Trust to complete a long-term 

 Management Plan for the 324-acre Kaweah Oaks Preserve in Tulare County. 

 Species benefited include the Valley elderberry longhorn beetle and willow 

 flycatcher. 

 7. Funds were provided to Ducks Unlimited to restore the natural hydrology to 

 support vernal pool and vernal pool-alkali meadow complex habitats on 431 

 acres on Tracts G & H of the Sacramento River National Wildlife Refuge in Glenn 

 County. Species benefited include palmate-bracted bird’s beak, hairy orcutt 

 grass, Greene’s tuctoria, Hoover’s spurge, vernal pool tadpole shrimp, 

 conservancy fairy shrimp, vernal pool fairy shrimp, and Swainson’s hawk. 

 8. Funds were provided to River Partners to assist with riparian habitat restoration 

 on 300 acres of fallow floodplain lands on the San Joaquin River National 

 Wildlife Refuge in Stanislaus County. Species benefited include Valley 

 elderberry longhorn beetle, riparian brush rabbit, riparian woodrat, least Bell’s 

 vireo, western yellow-billed cuckoo, and Swainson’s hawk. 

 9. Funds were provided to Environmental Science Associates to conduct baseline 

 research, GIS mapping, and predictive modeling to aid recovery of gabbro soils/ 
CVPIA – Annual Report for Fiscal Year 2006 29 

 Pine Hill listed plant species in El Dorado County. Species benefited include 

 Pine Hill ceanothus, El Dorado mule ears, Stebbins morning glory, and Pine Hill 

 flannelbush. 

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

 of 192 acres of grassland/alkali scrub habitat on Atwell Island in Tulare County. 

 Species benefited include Tipton kangaroo rat and San Joaquin kit fox.

Project Title: Management of Dedicated CVP Water for Environmental 

Purposes

 CVPIA Section 3406(b)(2) 

FY 2006 Funding: $1,000,000 

FY 2006 Accomplishments: 

On May 9, 2003, Interior released its “Final Decision on Implementation of Section 3406 (b)(2)” 

(Final Decision), in response to a ruling in March, 2002, by the Federal District Court. The Final 

Decision provided a calculation of CVP water, identified the method of accounting for use of 

the dedicated CVP yield [(b)(2) water] pursuant to the CVPIA, set out procedures for 

management of the water, and listed potential measures that may be prescribed by the Service 

for use of the dedicated water. The Final Decision was implemented beginning October, 2003, 

and was further clarified by a Department of the Interior memorandum, “Guidance for 

Implementation of Section 3406(b)(2) of the CVPIA,” dated December 17, 2003. 

Reclamation, Service, NOAA Fisheries Service, 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 (b)(2) water is part of that 

baseline and is closely coordinated with management of the EWA. 

Both (b)(2) water and the EWA contribute to the anadromous fish doubling goal, and provide 

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

Monitoring and evaluation to assess the effectiveness of implemented environmental measures 

under section 3406 (b)(2) of the CVPIA continues. 

FY 2006 accomplishments include the following: 

Prepared annual operations forecast representing 1992 baseline conditions and 1995 Water 

Quality Control Plan (WQCP) conditions. An annual 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. 

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

current accounting for the accounting year, as of the end of the previous month. Final 

accounting for all (b)(2) water actions for the entire water year was calculated by October 31. 

Included stakeholders and public input on the annual fishery action plan and how the plan was 

integrated into the operations forecast. 
CVPIA – Annual Report for Fiscal Year 2006 30 

Continued monitoring and evaluation of the effectiveness of (b)(2) water actions. 

Augmented base flows in Clear Creek throughout the year to improve habitat conditions for 

anadromous fish; including benefits to Chinook salmon and steelhead upstream migration, 

spawning, egg incubation, rearing, and downstream migration. 

It should be noted that water year 2006 was classified as a wet year type in both the Sacramento 

and San Joaquin Basins, and with the exception of Clear Creek, the need for instream (b)(2) 

actions was relatively small. (b)(2) water was used to augment base flows in the Sacramento 

and Stanislaus Rivers in December 2005 to improve habitat conditions for Chinook salmon and 

steelhead upstream migration, spawning, egg incubation, and rearing. Flood control operations 

on the Stanislaus River in the spring of 2006 precluded the need for additional (b)(2) water for 

spring outmigration flows for salmonids. 

Closed Delta cross channel gates December 3, 2005, to protect emigrating juvenile salmonids 

from the Sacramento basin, including listed Chinook salmon and steelhead. 

Reduced Delta exports April 26-May 3, 2006, to protect delta smelt (prior to the VAMP 

implementation period), and San Joaquin River emigrating salmonids. 

Reduced Delta exports May 3-June 2 to protect emigrating salmonids, delta smelt, and to 

facilitate VAMP in San Joaquin basin streams. 

 In response to relatively high salvage of juvenile salmon in the post-VAMP period, reduced 

Delta exports from June 6-June 22 to protect San Joaquin basin salmon and steelhead. 

Due to the wet hydrology in 2006 and the limited amount of water needed for protective fish 

actions, approximately 195,000 AF of (b)(2) water was banked in Shasta Reservoir for potential 

use in Water Year 2007, and 183,000 AF of (b)(2) water was made available for other project 

purposes. 

Since 1993, (b)(2) water has been dedicated and managed annually for fish, wildlife, and habitat 

restoration purposes; to assist the State of California in its efforts to protect the waters of the San 

Francisco Bay/Sacramento-San Joaquin Delta estuary; and to help meet post-1992 ESA 

requirements. 

In general, (b)(2) water actions have included: (1) instream flow augmentations on CVPcontrolled streams to protect salmon and steelhead and contribute toward meeting AFRP flow 

objectives; (2) increased releases from New Melones Reservoir to help meet Delta WQCP 

requirements for San Joaquin River flows at Vernalis; (3) increased releases from Shasta and/or 

Folsom reservoirs to help meet outflow requirements for the Delta WQCP; and (4) export 

reductions at the Central Valley Project’s Tracy Pumping plant to protect at-risk fish species 

(notably salmon, steelhead, and delta smelt). 

Many factors have contributed to the decline of anadromous fish in Central Valley rivers and 

streams. Pursuant to CVPIA and AFRP numerous restoration efforts have been implemented 

that are intended to positively affect more than one stressor, including the use of (b)(2) water to 
CVPIA – Annual Report for Fiscal Year 2006 31 

help meet AFRP flow objectives. Consequently, assessing the biological benefits of (b)(2) water 

actions in isolation from other restoration activities is very difficult. However, the Service 

believes increased instream flows, in particular, have helped maintain or improve salmon and 

steelhead habitat and populations in CVP-controlled streams. The Service also believes that 

export reductions at critical times have helped protect delta smelt as well as salmon and 

steelhead in the Delta. 

The (b)(2) water is just one of the environmental tools created by the CVPIA to achieve the 

AFRP anadromous fish doubling goal. The AFRP Restoration Plan establishes Chinook salmon 

doubling targets for each of the main rivers and streams in the Central Valley. On the CVPcontrolled streams, where (b)(2) water is available, only Clear Creek appears to be meeting the 

doubling goal for fall run Chinook. The Service is still evaluating whether the doubling of 

natural production will be sustainable on a long-term basis. Table 4 describes recent adult 

salmonid escapement trends on CVP-controlled streams relative to the anadromous fish 

doubling goal. 

Real-time fish monitoring helps inform (b)(2) water decisions on when and where actions 

should be taken. On a weekly basis, biologists from the Sacramento, San Joaquin, and Delta 

update the Data Assessment Team on fish movements. The sites sampled include the mainstem 

Sacramento and San Joaquin rivers, their major tributaries, and various locations in the Delta, 

including the export facilities. 

Table 3. Recent salmon and steelhead escapement trends in CVP-controlled streams, relative to 

the anadromous fish doubling goal. A “Yes” indicates that recent escapement trends meet or 

exceed the numeric doubling goal; however, sustainability of these escapement numbers is yet 

unknown. A blank field indicates that a specific goal has not been established. Note that 

striped bass, green sturgeon, white sturgeon, and American shad estimates are not included, 

and non-CVP controlled streams are not included. 

Table 3. Adult Salmonid Escapement Trends on CVP-Controlled Streams (anadromous fish 

doubling goal) 

 Fall-Run 

Chinook 

Salmon 

Late Fall-Run 

Chinook 

Salmon 

Winter-Run 

Chinook 

Salmon 

Spring-Run 

Chinook 

Salmon 

Steelhead 

Clear Creek Yes unknown 

Sacramento 

River 

No No No, but 

population 

increasing 

No unknown 

American River No 

Stanislaus River No 
CVPIA – Annual Report for Fiscal Year 2006 32 

Project Title: Water Acquisition Program

 CVPIA Sections 3406(b)(3) and 3406(g) 

FY 2006 Funding: $17,005,171 

FY 2006 Accomplishments: 

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

various means, water to supplement the 800,000 acre feet (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 2006, 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 Program and 

the San Joaquin River Agreement (SJRA). 

4. Acquire water to improve spawning and rearing habitat and increase migration flows 

for fall-, winter- and spring-run Chinook Salmon and steelhead, in support of the AFRP 

Restoration Plan and in coordination with the CALFED Environmental Water Program 

and Environmental Water Account 

Outstanding issues that need to be addressed include financial constraints on the acquisition of 

100 percent of Incremental Level 4 supplies, because of the increasing price of water and 

inadequate funding limits of the Restoration Fund. A summary of water purchases and 

executed agreements for FY 2006 is provided in Table 4. 

Table 4. Summary of water purchases and executed agreements for the Water Acquisition 

Program in FY 2006. Total cost for Fiscal Year 2006 includes funds obligated in FY 2005.

Delivery 

Period Seller 

Quantity 

(AF) Cost 

Cost per 

AF Purpose 

Oct 05 

SJR Group 

Authority/ 

Merced I.D. 

12,500 $212,375 $17 

Fall attraction flows and 

habitat improvement in 

Merced River and lower San 

Joaquin River (SJR) per SJRA. 

(FY04 and FY05 Funds) 

May-Jun 06 SJR Group 

Authority 110,000 $4,683,487 N/A 

Pulse Flows per SJRA/VAMP 

(FY05 and FY06 funds and state 

cost share) 

Apr-Sep 06 

SJR Group 

Authority/ 

Oakdale I.D. 

15,000 $900,000 $60 

Flow for habitat improvement 

in Stanislaus and lower San 

Joaquin Rivers 

Jun - Sep 06 SJR Group 11,000 $660,000 $60 Oakdale I.D. difference water 
CVPIA – Annual Report for Fiscal Year 2006 33 

Table 4. Summary of water purchases and executed agreements for the Water Acquisition 

Program in FY 2006. Total cost for Fiscal Year 2006 includes funds obligated in FY 2005.

Delivery 

Period Seller 

Quantity 

(AF) Cost 

Cost per 

AF Purpose 

Authority/ 

Oakdale I.D 

from VAMP 2005 (per SJRA). 

May – Jun 06 N/A N/A $302,307 N/A VAMP monitoring 

May 06 - Feb 07 Banta Carbona 

Water District 5,000 $675,000 $135 Level 4 refuge water, contract year 2006 

Jan 06 – Apr06 

KernTulare and 

Panoche Water 

District 

20,239 $2,833,460 $140 

Level 4 refuge water, contract 

year 2006. Acquired the water 

from Panoche and Kern Tulare 

conveyed, stored and 

exchanged the Panoche water 

for SWP water for delivery to 

Kern refuge. 

May 06-Feb 07 

Patterson 

Irrigation 

District 

9,000 $1,215,000 $135 Level 4 refuge water, contract 

year 2006 

-Feb 06 

San Joaquin 

River Exchange 

Contractors 

Water Authority 

49,583 $5,291,220 $107 Level 4 refuge water, contract 

year 2006 

TOTALS 232,322 16,772,849 

FY2006 accomplishments also include the following: 

1. Worked with the Interagency Refuge Water Management Team to develop water delivery 

schedules for Level 2 and incremental Level 4. 

2. Coordinated the refuges’ water needs and delivery schedules with Reclamation’s Central 

Valley Operations Office to ensure the refuges’ water needs are met. 

Refuge Benefits 

Prior to CVPIA, refuge management priority was fall flood-up and maintenance of adequate 

pond levels throughout the winter. Since 1992, supplemental refuge water supplies acquired by 

the Water Acquisition Program have provided a more consistent, reliable year round water 

supply to certain Central Valley refuges. Some of the benefits include: 

1. Increased frequency and acreage of irrigated moist soil food plants. The result has been 

a doubling in desirable plant biomass, which equates to more high-quality, high energy 

food available to waterfowl. 

2. Improved maintenance water flows through refuge ponds to improve water quality and 

reduce avian disease. 
CVPIA – Annual Report for Fiscal Year 2006 34 

3. Increased critical deepwater habitat within existing riparian zones. An example of 

biological benefits is establishment of a great blue heron rookery at Kern National 

Wildlife Refuge (NWR) in 1998. By 2001 there were 53 nests counted, inhabited by 

numerous nesting herons, egrets, cormorants and night-herons. 

4. Increased spring and summer habitat to benefit water dependent wildlife such as the 

giant garter snake. An example of habitat improvements occurred within Grassland 

Resource Conservation District (GRCD) consisting of 14,000 acres of additional spring 

habitat between 1991 and 2003 and 2,400 acres of additional summer habitat between 

1991 and 1998. 

5. Increased critical spring and summer breeding habitat for the white-faced ibis which is a 

“species of special concern.” At Sutter NWR the population of this species has increased 

from 50 in 1992 to over 15,000 in 2004, and at Kern NWR the population increased from 

50 in 1992 to over 8,000 in 2005. 

6. Increased early fall habitat for over-wintering migrants. Between GRCD, Kern NWR 

and Pixley NWR, there has been an increase in overall early fall habitat of 2,300 acres in 

2003 for the benefit of the northern pintail and other early migrants which arrive in 

August to over-winter. 

Groundwater Investigations

Groundwater investigations are being conducted by the Water Acquisition Program to lower 

the costs of providing supplemental refuge water supplies and to increase the reliability of these 

water supplies. In 2006, the Water Acquisition Program continued to conduct groundwater 

studies at Pixley NWR, East Bear NWR and Los Banos Wildlife Area to determine the potential 

for sustained use of groundwater resources on these refuges to meet Incremental Level 4 needs. 

Additional groundwater investigations will be conducted over the next several years at other 

refuges receiving water supplies pursuant to CVPIA. 

Instream Flows for SJRA and VAMP 

The Water Acquisition Program has acquired water from the San Joaquin River Group 

Authority (SJRGA) and its member agencies to provide additional spring and fall fishery flows 

on the Stanislaus, Tuolumne, Merced, and lower San Joaquin rivers. This water is acquired in 

support of the SJRA and VAMP, which is a scientifically based fishery management plan to 

determine the relationships between flows, exports, and other factors on fish survival in the 

Sacramento-San Joaquin Delta. The increased flows benefit numerous resident and 

anadromous fish species but are acquired primarily to benefit Chinook salmon. Central Valley 

Chinook salmon constitute the majority of salmon produced in California, and at times have 

accounted for 70 percent or more of the statewide commercial harvest. The SJRA and VAMP 

will continue as an on-going requirement until at least 2009. 

Instream Flows for AFRP 

The AFRP identified the need to augment stream flows on some tributaries to the Sacramento 

and San Joaquin rivers to help meet a doubling goal of Central Valley anadromous fish 

identified in Section 3406 (b)(1) of CVPIA. In recent years, the Service has led a planning effort 

to determine which tributaries should receive priority for instream acquisition efforts. A key 
CVPIA – Annual Report for Fiscal Year 2006 35 

product of this effort is a Decision Support Model (DSM). The DSM evaluates key factors 

including potential biological benefits, availability of water rights, cost of water, and impacts, in 

order to assess water acquisition priorities. A monitoring component will be built into future 

instream acquisitions to assure flow requirements are met and biological benefits are quantified. 

A specific timeline for implementation of instream acquisitions in support of AFRP has not yet 

been established. 

Project Title: Tracy Pumping Plant Mitigation Program

 CVPIA Section 3406(b)(4) 

FY 2006 Funding: $2,243,795 

FY 2006 Accomplishments: 

The purpose of the Tracy Pumping Plant Mitigation Program (TPPMP) is to mitigate for 

impacts associated with the operation of the Federal Tracy (“Jones”) Pumping Plant located in 

the south Delta. Included within the scope of the TPPMP are research activities to determine 

improved methods of salvaging and handling fish at the Tracy Fish Collection Facility (TFCF) 

and implementation of operational and maintenance changes at the TFCF to provide 

improvements in salvage effectiveness. 

The current focus of the mitigation program is to improve fish protection and fish salvage at the 

existing TFCF facility as per federal ESA OCAP Biological Opinions and CALFED South Delta 

Fish Facility Forum (SDFF) recommendations. 

The SDFF recommended to hold off on construction of a large scale test facility (TFTF) to be 

located at Tracy and to, instead, focus on improving existing fish salvaging facilities in the south 

Delta, while implementing other less costly alternatives to fish protection. 

FY 2006 accomplishments include the following: 

1. Continuation of whole facility evaluations utilizing Delta smelt. 

2. Continued evaluation of the Tracy mitten crab traveling screen as a potential device for 

continuous woody and leafy debris removal while adequately passing fish. 

3. Continuation of studies on tracking predator fish movements inside fish salvage 

facilities using remote telemetry. 

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

collections tanks. 

5. Evaluation of stress on winter-run Chinook salmon associated with fish holding. 

6. Evaluation of above ground holding tank in the lab in Denver. 

7. Completed assessment of the historical 10-minute count screen used for estimating fish 

salvage. 
CVPIA – Annual Report for Fiscal Year 2006 36 

8. Continued development of fish taxonomic keys for various delta fish species. 

9. Maintenance and updating of a technical web site. Added technical guide for recently 

listed green sturgeon. 

FY 2006 improvement activities were: 

1. Completed rehabilitation of the Collection Tank Building and Northside Utilities. 

2. Completed evaluation and design of improved trash rack cleaning device for award in 

2007. 

3. Continued conceptual evaluation and design of improved primary and secondary 

louver cleaning system. 

It is difficult to summarize biological benefits of the TPPMP since 1992 due to uncertainty about 

how best to proceed in the south Delta to improve fish protection at both the Federal TFCF and 

State J.F. Skinner Fish Facility. Originally the plan was to construct a full scale (i.e. 2,500 cfs) 

TFTF as one-half of the eventual replacement of the existing TFCF and phase in construction of 

several 2,500 cfs modules at the Skinner facility also. However, due primarily to exorbitant 

construction costs, the CALFED SDFF recommended focusing more on improving the existing 

fish facilities to bring them back into original design compliance, as best as possible, while 

implementing other less costly fish protection and restoration measures elsewhere within the 

state. 

The research activities conducted as part of the TPPMP provide valuable information towards 

future improvements in fish protection at the South Delta fish facilities (both the CVP and 

SWP). 

Once present research efforts are completed, or as they are being completed, physical and/or 

operational changes will be made at the existing facilities to improve efficiency of the fish 

salvage process. Additionally, field tests will be conducted after implementation to assess the 

effectiveness of these changes. 

It is anticipated that at least three to five more years of intensive field and lab testing is required 

to determine best methods of salvaging fish at the TFCF under the current conditions. Some 

improvements can be implemented sooner than others. 

Since the overall efficiency of the federal TFCF has lessened by as much as 60 percent over the 

past 40+ years, it is anticipated that the improvements will result in substantial fish savings 

although exact numbers are difficult to quantify due the rather large and complex design of the 

TFCF. 
CVPIA – Annual Report for Fiscal Year 2006 37 

Project Title: Contra Costa Canal Pumping Plant Fish Screen Project

 CVPIA Section 3406(b)(5) 

FY 2006 Funding: $214,303 

FY 2006 Accomplishments: 

This Program provides 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 the Service’s biological opinion for the delta smelt that 

was issued for the Los Vaqueros Project. 

With the development of alternative short-term fishery mitigation measures, Reclamation 

presented these measures to the Service, Fisheries Service, and CDFG, with a request for an 

amendment to the Los Vaqueros biological opinion 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 adding mitigation requirements. 

Final design and construction of a major project at the Contra Costa Canal Pumping Plant will 

await the results of further studies by the Contra Costa Water District and responses from the 

fishery and regulatory agencies on an amendment to the biological opinion. 

A Fish Monitoring 

1. With the assistance of State of California Department of Fish and Game (CDFG) drafted 

an improved monitoring program. Implementation of the plan began in FY2004 and will 

continue indefinitely. Regular sampling through FY 2006. 

2. Entered into a new agreement with Contra Costa Water District contracted for the 

monitoring of the Rock Slough. 

B. Regulatory Process 

1. The US Fish and Wildlife Service (USFWS) drafted a letter permitting our operation through 

the year 2008 in the absence of a screening facility. This includes mitigation for each year that 

Reclamation extends./survey actions related to listed species impacted by the CVP. 

2. Completed first mitigation action through the Contra Costa County HCP and entered into an 

agreement for FY2005. 

C. Design 

No new design activities in this fiscal year beyond the ad hoc design team formation and a 

search of literature. 

D. Secured a determination from the Solicitors related to CVPIA 3406(b)(5); summarized here: 

Section 3406(b)(5) clearly and unequivocally states that "[t]he Secretary . . . is authorized and 

directed to . . . develop and implement a program to mitigate for fishery impacts resulting from 

operation of the Contra Costa Canal Pumping Plant No. 1. Such program shall provide for 

construction and operation of fish screening and recovery facilities . . ." Failure to construct or 

failure to take reasonable actions toward completion of the fish screen required under CVPIA 

3406(b)(5) may expose the Secretary to a lawsuit for injunctive relief. Administrative 

Procedures Act, section 701(1) of title 5 of the United States Code, provides that a federal court 

may "compel agency action unlawfully withheld or unreasonably delayed." 
CVPIA – Annual Report for Fiscal Year 2006 38 

Project Title: Flow Fluctuation/Reservoir Storage Management Program

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

FY 2006 Funding: $ 50,000 

FY 2006 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 on 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. Although no funding specifically allocated for section (b)(19), reservoir storage was 

studied under 3406(b)(2) in FY 2006. 

The American River Operations Work Group met monthly throughout FY 2006 to discuss 

American River operations and to determine threshold flows and ramping rates required to 

protect Lower American River 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 still ongoing. An early 

draft report of that study was released in July, 2004. More regular discussions of the Operations 

Group are held in the April/May period when the pulse flows for 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 2006 Funding: $1,082,000 

FY 2006 Accomplishments: 

CVPIA Section 3406(b)(10) requires the development and implementation of measures 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 (SNWR). 

Substantial improvements in both matters occurred independently of the CVPIA in the early to 

mid 1990's. Installation of a siphon under Stony Creek, made the Glenn Colusa Irrigation 

District's Canal a reliable means of conveyance of water to the SNWR and NOAA Fisheries 

Service’s 1993 biological opinion for the winter-run Chinook salmon, which required a lifting of 

the RBDD gates between September 15 and May 15, eliminated most of the fish passage 

problems. 

Further improvements are possible since about 80% of the adult Spring run Chinook salmon 

population at RBDD and approximately 50% of the adults of the southern population of the 
CVPIA – Annual Report for Fiscal Year 2006 39 

green sturgeon are delayed or blocked when attempting to move upstream of RBDD. However, 

the magnitudes of the benefits are unclear. On the one hand, only 8% of the overall spring-run 

population is affected, as is roughly half of the green sturgeon population. However, the 

spawning conditions downstream of RBDD appear to be suitable for green sturgeon, and it is 

unclear how significant either fish passage problem is relative to other fishery needs. 

Further improvements would require major changes in infrastructure to prevent violation of 

water service contracts and disruption of agricultural production, given the high demand for 

water in late May. Meeting that demand upon further raising the gates would require so much 

pumping capacity that a pumping plant meeting the demand in late May would be large 

enough to meet water demands any time in the year. Anything less, would devastate 

agriculture. Building a new, large pumping plant would cost an estimated 130 million dollars in 

2006 dollars, given the recent increases in the costs of concrete and steel. 

Formal decisions are still pending completion of an Environmental Impact 

Statement/Environmental Impact Report (EIS/EIR) and Record of Decision for the RBDD Fish 

Passage Program Improvement Project. The draft EIS/EIR, which focused on structural 

alternatives to resolve fish passage problems at RBDD, was made available for public review in 

2002. Work was then suspended pending, first, completion of ESA section 7 consultation for the 

Central Valley Project Operations Criteria and Plan (OCAP) and, second, completion of the 

Long Term Water Contract Renewal process. Consequently, little was done on fish passage 

improvements pending completion of the Endangered Species Act consultations for the CVP as 

a whole, although installation of a fourth pump in the Research Pumping Facility at RBDD was 

completed to help alleviate water delivery problems associated with current gate operations, 

and the fish monitoring equipment in the RBDD fish ladders was upgraded. 

Project Title: Coleman National Fish Hatchery

 CVPIA Section 3406(b)(11) 

FY 2006 Funding: $270,000 

FY 2006 Accomplishments: 

Section 3406(b)(11) of the CVPIA states that the Secretary is authorized and directed to 

rehabilitate and expand the Coleman National Fish Hatchery (NFH) by implementing the 

Service’s Coleman National Fish Hatchery Station Development Plan, and modify the Keswick 

Dam Fish Trap to provide for its efficient operation at all project flow release levels and modify 

the basin below the Keswick Dam spillway to prevent the trapping of fish. Coleman NFH was 

originally constructed in 1942 to offset fish habitat losses resulting from the construction of 

Shasta and Keswick dams (the cornerstone of the CVP). 

In FY 2006 CVPIA funding was received from Reclamation for the design and construction of a 

visitor kiosk and informational panels at the Coleman National Fish Hatchery. This work is 

consistent with requirements of Phase 9 of the Coleman National Fish Hatchery Station 

Development Plan. Contract specifics for this project include; 

1. Construct one informational/educational kiosk. The kiosk should have an area of 

approximately 500 square feet. The kiosk should be constructed of wood, metal, or a 

combination of each. The kiosk should comply with all necessary building and safety codes. 
CVPIA – Annual Report for Fiscal Year 2006 40 

2. Construct educational/signs and display boards for the kiosk covering topics such as: 

a. Welcome and Orientation. This includes a brief history of the hatchery, a 

welcoming statement, and a map of the area and the hatchery. 

b. What We Do. The purpose of the hatchery, why it is operated and brief 

descriptions of what is done. 

c. Upper Sacramento River Salmonids. History and biology of Central Valley 

salmon and steelhead, measures taken through the Central Valley Project 

Improvement Act, CALFED and other programs to improve salmon and 

steelhead populations. 

3. Other educational signs/placards located throughout the hatchery grounds to interpret 

various facilities, buildings, operations or topics. 

Reclamation executed the funding document with final signature on July 17, 2006. In FY 06 

these funds were transferred to the Service’s Visitor’s Services Program in Portland for contract 

execution. Project reconnaissance will begin in FY 2007, with project completion expected by 

December 2008. 

Project Title: Clear Creek Restoration Program

 CVPIA Section 3406(b)(12) 

FY 2006 Funding: $833,101 ($125,000 WRR; $708,101 restoration fund of which 

 $408,101 came from AFRP to conduct IFIM study) 

FY 2006 Accomplishments:

This section of the Act requires 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 from Whiskeytown Dam to allow sufficient spawning, incubation, 

rearing, and outmigration for salmon and steelhead. 

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

efforts on Clear Creek have focused on improving instream habitat conditions for anadromous 

salmonids. 

 

FY 2006 accomplishments include the following: 

Monitoring showed a more than 400 percent average increase in spawning density in Phase 3A 

of the stream channel restoration project. 

Designs and proposal for stream channel restoration project 3B submitted to CALFED were 

accepted for funding for Phase 3B of the stream channel restoration project. 

Point Reyes Bird Observatory monitoring indicated that migratory songbird diversity and 

population sizes were increasing in the restoration area. 

IFIM data collection for rearing habitat was completed in the upper half of the anadromous 

reach below Whiskeytown Dam. 
CVPIA – Annual Report for Fiscal Year 2006 41 

Flows were provided suitable for all life stages of anadromous salmonids. 

Fall-run Chinook salmon escapement was approximately 8,422. 

Threatened spring-run Chinook salmon continued to repopulate upstream reaches. 

Threatened steelhead spawning continues to concentrate in injected spawning gravel. 

Completed the Clear Creek Decision Analysis Model to estimate the amount of annual gravel 

additions needed to maintain spawning gravel supply after the creek has been recharged to 

eliminate 43 years of accumulated gravel deficit. 

Constructed temporary barrier weir to prevent fall-run Chinook salmon from hybridizing with 

spring-run Chinook salmon. 

Added 2,700 tons of spawning gravel to the National Environmental Education (NEED) Camp 

site, and developed designs for Dog Gulch and Peltier Valley Road Bridge. 

Monitoring indicated that temperature criteria for spring-run Chinook salmon spawning were 

exceeded for the majority of the spawning period but only by a biologically minor increment. 

Completed “Mercury Synthesis and Data Summary Report for Lower Clear Creek: Shasta 

County, CA.” 

Project Title: Spawning Gravel Replenishment Program

 CVPIA Section 3406(b)(13) 

FY 2006 Funding: $500,000 

FY 2006 Accomplishments: 

The Central Valley Project Improvement Act (CVPIA) directs that a program be established to 

replenish anadromous fish spawning gravel that has been lost as a result of the construction 

and operation of the Central Valley Project, bank protection projects, and other activities on the 

Sacramento, American, and Stanislaus rivers. Since 1997, the gravel replenishment program 

mandated in section 3406(b)(13) of the CVPIA has implemented actions that placed 

approximately 170,000 tons of spawning gravel in these rivers to increase the availability of 

spawning 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. 

Approximately 154,000 tons of spawning gravel has been placed in the upper Sacramento River 

since 1997. A total of 34,000 tons of gravel has been placed at a site on the west bank, 

immediately downriver from Keswick Dam, during the years 1997, 1998, 2000, 2004, 2005, and 

2006; 96,300 tons at a site on the west bank, immediately downstream from the confluence with 

Salt Creek, during the years 1997, 1998, 1999, 2002, 2003, 2004, and 2005; and 23,000 tons on the 

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

2000. These introductions have occurred in anticipation that subsequent high river flows will 

disperse the gravel downriver. In every case the gravel has been dispersed. 
CVPIA – Annual Report for Fiscal Year 2006 42 

The substrate at three riffles on the lower American River was manipulated and 6,000 tons of 

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

A total of 10,000 tons of spawning gravel has been placed in the Stanislaus River since 1997 at 

several sites immediately downriver from Goodwin Dam. On two occasions, helicopters were 

used to deposit the gravel directly into the channel. Gravel was also delivered by truck to areas 

adjacent to the channel, and pushed into the river channel. Gravel was deposited into the river 

channel in 2004 by means of a sluice delivery system. The introduced gravel was subsequently 

dispersed downriver by streamflow. 

Selected cobble at the Upper Sacramento River placement site in the vicinity of Salt Creek was 

implanted with electronic monitors to follow the downriver movement of gravel. Monitoring 

was conducted for one season. Field observations indicated the cobble moved varying 

distances downriver, with the farthest movement reaching to just above Anderson Cottonwood 

Irrigation District Diversion Dam at the City of Redding. Visual anecdotal observations have 

similarly been reported for adult salmon spawning in the vicinity of the gravel and for large 

numbers of juvenile salmon adjacent to the gravel placement sites. Aerial redd surveys 

unrelated to this program have indicated that winter-run Chinook salmon spawning 

distribution has shifted upstream since gravel introductions began in the upper river near 

Keswick Dam. A high proportion of winter run Chinook spawn on the placed gravel. 

Gravel placement in the American River occurred in 1999, and monitoring has been conducted 

since then as a part of the 1999 plan to evaluate the project before designing new gravel 

enhancement projects in the river. The monitoring has shown that Chinook salmon spawning 

has occurred each year on the gravel placement sites at Sailor Bar and Sacramento Bar. 

Spawning at the Sunrise site occurs primarily during higher flows than are typical during the 

Chinook salmon spawning period; however, steelhead have spawned on the gravel at Sunrise 

during higher flow periods. The average Chinook salmon escapement from 2001 through 2005 

(148,000) was more than triple the average escapement prior to that period (42,000). Although 

the increase in escapement has been substantial following the project, the increase cannot be 

attributed to the gravel project. The hatchery contributes a large, unknown portion of Chinook 

salmon production, and favorable ocean conditions enhanced marine survival over the period 

since gravel placement. Monitoring of adult Chinook salmon spawning activity during 2005 

showed that fish densities during the peak spawning period in the upper river are higher than 

needed to fully utilize the existing spawning habitat. Many of the ‘extra’ salmon died prior to 

spawning, likely due to competition with fish that successfully defended favorable spawning 

sites and spawned. New gravel replenishment projects are currently being pursued in the 

American River. 

Prior to gravel placement in Goodwin Canyon, spawning habitat was extremely limited in the 

upper four miles of the Stanislaus River, and little spawning occurred there. Since gravel 

placement began, approximately 150 female Chinook have spawned in Goodwin Canyon each 

year on the new gravel. This number of Chinook salmon spawners should produce about 

745,000 eggs, which in turn should produce about 400 adult Chinook salmon, annually in the 

Stanislaus River. The area of the Stanislaus River near Goodwin Canyon contains the best water 

quality year-round for salmonids because the water is cooler than that farther downstream. In 
CVPIA – Annual Report for Fiscal Year 2006 43 

addition, steep sections of river prevent predatory fish from migrating to Goodwin Canyon. 

Because of the cooler temperatures and lack of predation, salmonids that spawn in the upper 

river, where the gravel enhancement has occurred, likely produce more outmigrating smolts 

per spawner than those that spawn lower in the river. In addition to spawning habitat values, 

gravel placement enhances rearing habitat conditions for salmonids. Juvenile rearing densities 

on the new gravel are roughly double that of other rearing habitat in close proximity.

FY 2006 accomplishments include the following: 

1. A total of 6,000 tons of spawning gravel was delivered and placed in the river at the 

Keswick Dam site on the Sacramento River. Initiated a spawning gravel monitoring 

program to evaluate the effectiveness of augmentation projects. Completed an 

annotated bibliography of previous gravel restoration documents/studies. Mapped 

current and historic spawning gravel restoration sites and fluvial habitat. Surveyed the 

longitudinal channel profile. A high proportion of winter run Chinook spawn on the 

gravel injected in the upper river. 

2. Continued the spawning gravel monitoring program. on the lower American River 

which included two items: (1) aerial photo documentation of Chinook spawning 

locations and redd densities relative to gravel placement sites on three dates throughout 

the spawning period; and (2) spawning gravel condition monitoring to assess suitability 

of spawning gravels in the gravel placement sites and in other high use spawning areas, 

compared to low use and unused habitats. Initiated a gravel budget for the Lower 

American River to determine what comes in versus what becomes unavailable regarding 

spawning gravel supply. Continued gravel permeability studies. 

3. Placed 1,500 tons of spawning gravel at placement sites in Goodwin Canyon on the 

Stanislaus River. Pre-placement and post-project streambed topography was mapped 

through the reach of spawning gravel placement so physical characteristics of the habitat 

can be monitored over time. Redds were mapped at the gravel placement sites in 

Goodwin Canyon. Snorkel surveys were conducted at placement and reference sites to 

evaluate salmonid use of the restored sites. Underwater observations verified that fry 

emergence occurred from the placed gravels, and rearing densities were high. 

The vision for this program is to replenish gravel in the three designated rivers to maintain 

sufficient salmon and steelhead spawning habitat in support of CVPIA goals. The dams on 

these rivers have created a permanent block to gravel recruitment downstream of the dams, and 

the remaining sources of gravel are limited to tributary inputs and side-bank erosion 

downstream of the dams, both of which cannot replenish these losses on their own. 

Consequently, it is anticipated that the gravel replenishment requirements of the Gravel 

Replenishment Program will remain in place into the future, for as long as gravel recruitment is 

curtailed. 
CVPIA – Annual Report for Fiscal Year 2006 44 

Project Title: Comprehensive Assessment and Monitoring Program

 CVPIA Section 3406(b)(16) 

FY 2006 Funding: $500,000 

FY 2006 Accomplishments:

The Comprehensive Assessment and Monitoring Program (CAMP) was established pursuant to 

Section 3406(b)(16) of the CVPIA. The goal of the program is to monitor fish and wildlife 

resources in the Central Valley and to assess the biological results and effectiveness of actions 

pursuant to Section 3406(b) of the CVPIA. The CAMP has two objectives: 

1. Assess the overall (cumulative) effectiveness of actions implemented pursuant to CVPIA 

Section 3406(b) in meeting fish production targets that have been quantified by the 

Anadromous Fish Restoration Program (AFRP), and 

2. Assess the relative effectiveness of categories of Section 3406(b) actions (e.g., water 

management modifications, structural modifications, habitat restoration, and fish 

screens) toward meeting AFRP fish production targets. 

In FY 2006, CAMP accomplished the following activities: 

1. A new manager and technical assistant were hired to manage the program and develop 

more effective strategies for achieving the abovementioned objectives, and 

2. The CAMP provided funding or partial funding and management for eight projects that 

were designed to monitor the abundance of anadromous fish. Funding for these 

projects was derived from CAMP and an Anadromous Fish Restoration Program 

(AFRP) accounts managed by the Sacramento Fish and Wildlife Office. These funds 

collectively totaled $533,465. The eight projects and costs included: 

a) Purchasing a digital video recorder (DVR) to assess salmonid escapement levels on 

Battle Creek ($10,000). After the DVR was purchased, staff from the Red Bluff Fish 

and Wildlife Office (RBFWO) assessed the utility and cost effectiveness of using 

the device to estimate salmonid escapement levels. The study with the DVR 

suggests the device can be used to monitor salmonid escapement levels and 

provide an enhanced ability to archive and recover escapement data. 

b) Collecting data to quantify habitat features that are important to juvenile steelhead 

and spring-run Chinook salmon in Clear Creek ($75,000). These data will 

ultimately be used to develop habitat suitability indices for juvenile salmonids and 

predict which flow regimes promote increases in the production of young 

salmonids on Clear Creek. 

c) Preparing a report quantifying production of juvenile salmonids from Battle 

Creek ($35,000). RBFWO staff prepared a report quantifying the number of 

juvenile steelhead and Chinook salmon that emigrated from Battle Creek 
CVPIA – Annual Report for Fiscal Year 2006 45 

between 1998 and 2001. The report was based on rotary screw trap data, and 

provides a basis for assessing the effectiveness of habitat restoration activities 

in that watershed. 

d) Conducting a winter-run Chinook salmon carcass survey on the Sacramento 

River ($108,000). RBFWO staff conducted a carcass survey to assess the 

abundance, migration timing, spawning distribution, and life history 

characteristics of adult winter-run Chinook salmon on a portion of the 

Sacramento River during the 2006 spawning season. Data from this study 

provide a basis for determining if the AFRP’s winter-run Chinook salmon 

production target was met in 2006. 

e) Collecting data and developing a report quantifying production of juvenile

salmonids from the Stanislaus River ($50,824). The Cramer Fish Sciences (CFS) 

consulting company was hired to operate two rotary screw traps on the 

Stanislaus River. These data were subsequently summarized in a report 

estimating the number of juvenile fall-run Chinook salmon and steelhead that 

were produced from the Stanislaus River in 2007. The rotary screw trap data 

will be used to assess effectiveness of habitat restoration activities on the 

Stanislaus River. 

f) Collecting data and developing a report quantifying production of juvenile 

Chinook salmon from the Merced River ($160,060). CFS was hired to operate 

two rotary screw traps on the Merced River. These data were subsequently 

summarized in a report estimating the number of juvenile fall-run Chinook 

that were produced from the Merced River in 2007. The rotary screw trap data 

will be used to assess the effectiveness of habitat restoration activities on the 

Merced River. 

g) Maintaining a “Chinookprod.xls” spreadsheet quantifying production of adult 

Chinook salmon from the Central Valley. This activity is a CAMP 

responsibility that primarily was performed by AFRP staff in the Stockton Fish 

and Wildlife Office. This spreadsheet provides production estimates for adult 

Chinook salmon from 22 watersheds in the Central Valley. The spreadsheet is 

available on the Internet at: http://www.delta.dfg.ca.gov/afrp/. 

h) Collecting data quantifying habitat features that are important to juvenile 

Chinook salmon and steelhead on the lower American River, Sacramento 

River, and the Sacramento-San Joaquin River Delta ($94,581). The data from 

this project provide a baseline for measuring the effects of future restoration 

activities. 

Project Title: Anadromous Fish Screen Program

 CVPIA Section 3406(b)(21) 

FY 2006 Funding: $ 9,979,879 

FY 2006 Accomplishments: 
CVPIA – Annual Report for Fiscal Year 2006 46 

The Anadromous Fish Screen Program (AFSP) serves two functions in its efforts to protect 

juvenile anadromous fish from the effects of unscreened water diversions. First, it is a 

potential source of cost-share funding for 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 by the AFSP. The AFSP funds 

are expended on a biological priority basis that is closely coordinated with the CALFED 

Environmental Restoration Program (ERP), 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 

participating diverters throughout various phases of project planning and implementation. 

The overall benefits of screening diversions as carried out by the AFSP include the 

following: 

 

1. Prevents entrainment of important fish species including steelhead and Chinook 

salmon. 

2. Compliments other fish habitat restoration efforts for anadromous fish. 

3. Meets legal requirements under the Endangered Species Act (ESA) to avoid or limit 

take of listed fish. 

The AFSP has funded fish screen projects at water diversions ranging from 17 to 1,000 cfs. 

Projects funded by the AFSP require a multi-year effort, with funds being provided for 

feasibility studies, engineering and design, construction, and start-up testing. 

Consequently, accomplishments reported in any given year may be the result of funding 

provided several years earlier. Through FY 2006, the AFSP has provided funding towards 

the construction of 22 completed fish screens. Approximately 3,300 cfs of diverted water in 

Central Valley streams is now fish-safe as a result. 

FY 2006 accomplishments include the following: 

1. Completed construction of a 100 cfs retractable cylindrical fish screen at Reclamation 

District 999 on the Sacramento River near Clarksburg. 

2. Continued to support construction activities of the Sutter Mutual Water Company 

Tisdale Pumping Plant Fish Screen project in Sutter County to screen a 960 cfs on the 

Sacramento River. 

3. Initiated construction of fish screen project at Reclamation District 108 to 

screen three diversions at a consolidated 300 cfs diversion on the Sacramento 

River in Colusa County. 

4. Continued to support screen design and environmental compliance activities for the 

Natomas Mutual Water Company (NMWC) Fish Screen project located on the 

Sacramento River in Sacramento County, to consolidate and screen five diversions 

totaling approximately 630 cfs. 
CVPIA – Annual Report for Fiscal Year 2006 47 

5. Continued to support screen design and environmental compliance activities for the 

Meridian Farms Water Company (MFWC) Fish Screen project in Sutter County to 

consolidate and screen three existing diversions totaling 165 cfs on the Sacramento 

River. 

6. Continued to support screen design and environmental compliance activities for the 

Reclamation District 2035 Fish Screen project located north of the City of Sacramento 

to screen a 400 cfs diversion on the Sacramento River. 

7. Continued to support screen design and environmental compliance activities for 

Patterson Irrigation District Fish Screen to screen a 190 cfs diversion on the San 

Joaquin River. 

8. Provide support for screen design and environmental compliance activities for the 

City of Yuba City Fish Screen project in Yuba County to screen a 61 cfs municipal 

diversion on the Feather River. 

Project Title: Trinity River Restoration Program

 CVPIA Section 3406(b)(23) 

FY 2006 Funding: $10,786,000 

FY 2006 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. This 

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, section 3406(b)(23) directed Interior 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 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, which 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 Record of Decision (ROD) was signed in 

December, 2000. The decision called for a range of flows from 369,000 acre-feet in critically dry 

years to 815,000 acre-feet in wet years to be released down the Trinity River. It also called for 

physical channel rehabilitation and coarse sediment augmentation to work in concert with the 

increased flows to restore habitat. Litigation that constrained Lewiston Dam releases since the 

signing of the ROD has been resolved and full implementation of the program is now 

underway. Dam releases for fishery purposes have increased from 340,000 acre-feet when the 

ROD was signed in 2000, to 815,000 acre-feet in 2006. 
CVPIA – Annual Report for Fiscal Year 2006 48 

In order to implement the increased dam releases, at risk manmade structures in the floodplain 

needed to be addressed. Modifications to four river crossings and the removal of at least one 

house were identified. In FY 2004 construction contracts were awarded for all four bridge 

projects with the new crossings opened to traffic early in Calendar Year 2005. The home at risk 

was purchased in March 2005 to allow for the largest fishery release (7,000 cfs) since 

construction of the Trinity River Division. 

FY 2006 accomplishments include the following: 

 

1. Contract award for construction of four channel rehabilitation projects downstream of 

Canyon Creek. Over 90,000 cubic yards of material was excavated along a 5-mile section 

of the Trinity River near Junction City, California. This will provide increased 

geomorphic and hydraulic complexity to this area of the river and provide greater 

diversity of fish habitats supporting a wide range of life history stages. 

2. Initiation of environmental documentation and preliminary designs for construction of 

eight other channel rehabilitation sites downstream of Lewiston Dam. Research shows 

that a four-fold increase in rearing habitat is required to obtain a doubling in fish 

populations. In all, 47 separate channel rehabilitation projects are scheduled for 

construction by 2012. 

3. Revegetation of native riparian habitat associated with the Hocker Flat Channel 

Rehabilitation Project constructed in 2005 to fulfill mitigation requirements and improve 

plant diversity. 

4. Construction of a channel rehabilitation site adjacent to the Trinity River Fish Hatchery, 

including the placement of 2,500 tons of spawning gravel. 

5. Removal of a private residence in fishery flow inundation zones. 

6. Initiation of a water and sewer system landowner assistance program to address 

facilities impacted by higher fishery flows. 

In general, program activities have resulted in improvements in juvenile and adult fish health 

since 1992. Increasing summer baseflows from 300 cfs to 450 cfs has improved temperature 

characteristics for juvenile steelhead, increasing overall health and reducing mortality as 

evidenced by data from outmigrant traps and estuary seining. Coho salmon populations in the 

Klamath/Trinity system have remained steady, as compared to other river systems along the 

California/Oregon coast that have experienced declines. Adult steelhead populations increased 

dramatically in 2006 and as large or larger of a run is predicted in 2007. 
CVPIA – Annual Report for Fiscal Year 2006 49 

Project Title: San Joaquin River Comprehensive Plan

 CVPIA Section 3406(c)(1) 

FY 2006 Funding: $2,000,000 

FY 2006 Accomplishments: 

In November 1989, Reclamation was directed by the Secretary of the Interior to explore 

opportunities for environmental restoration in the San Joaquin River Basin, as described in the 

San Joaquin River Basin Resource Management Initiative (Initiative). In November 13, 1991, 

Reclamation and the State of California’s Resource Agency (Agency) entered into a 

Memorandum of Agreement for “Sharing of the Cost of the San Joaquin River Basin Resource 

Management Initiative.” Among other things, the study activities described in the MOU stated 

“Reclamation and the Agency shall develop a mutually acceptable plan of study for the 

Initiative which is consistent with the work activities underway in the California Department of 

Water Resources’ San Joaquin River Management Program (SJRMP) effort.” It also stated the 

Initiative “...shall focus primarily on Chinook salmon, water quality conditions, wetlands for 

waterfowl, wildlife, reservoir fishery, and recreation...” 

Subsequently, in 1992, section 3406(c)(1) of the CVPIA mandated the preparation of a 

“reasonable, prudent, and feasible” comprehensive plan (Comprehensive Plan) to “address fish, 

wildlife, and habitat concerns on the San Joaquin River, including but not limited to the 

streamflow, channel, riparian habitat, and water quality improvements that would be needed to 

reestablish where necessary and to naturally reproducing anadromous fisheries from Friant 

Dam to its confluence with the San Francisco Bay/Sacramento-San Joaquin Delta Estuary.” 

Work under the scope of the Initiative was halted and efforts to develop a plan of action to 

develop the Comprehensive Plan were initiated by Reclamation and the Service. The CVPIA 

requires that “...Such plan shall be developed in cooperation with the California Department of 

Fish and Game and in coordination with the San Joaquin River Management Program [SJRMP] 

under development by the State of California; shall comply with and contain any documents 

required by the National Environmental Policy Act and contain findings setting forth the basis 

for the Secretary’s decision to adopt and implement the plan as recommendations concerning 

the need for subsequent Congressional action, if any...” 

 

In 1998, the Natural Resources Defense Council (NRDC) sued Reclamation (NRDC v. Rodgers,

No. CIV. S-88-1658 LKK/GGH) over the renewals of long-term water service contracts in the 

Friant Division of the CVP. The Friant Water Users Authority (FWUA) intervened in the suit. 

In an effort to settle this litigation, on October 25, 1999, in response to a jointly signed letter from 

the NRDC and FWUA, CVPIA Restoration Funds were provided to assist NRDC and the 

FWUA in their San Joaquin River restoration planning activities. Thus, the Reclamation and 

Service led effort to develop a Comprehensive Plan was re-focused to support the 

FWUA/NRDC approach. Their efforts were funded in a large part from CVPIA Restoration 

funds and California Proposition 13 funds. Restoration funds were provided for this purpose 

since the information developed would assist Interior in the development of the required 

Comprehensive Plan. 

Although the San Joaquin River Riparian Habitat Restoration Program (SJRRHRP) was 

established in 1997 and functioned as a six-party, consensus-based management team directing 

short-term projects that would provide useful baseline data for Interior’s overall efforts to 

gather existing conditions data on the San Joaquin River, it became a complimentary program 
CVPIA – Annual Report for Fiscal Year 2006 50 

for specifically defined demonstration efforts, programs, and studies the FWUA and NRDC 

restoration planning also requested. 

 

When FWUA and NRDC ended their restoration planning efforts in 2004, the approach to 

develop a Comprehensive Plan was re-directed again to have Reclamation and the Service lead 

the effort in FY 2005. To administratively reflect the continuing Interior focus to develop a 

Comprehensive Plan, $1 million of the $1.5 million provided under Section 3406(b)(1) was 

provided to Section 3406(c)(1) to clearly convey that all San Joaquin River restoration planning 

efforts are for the Comprehensive Plan development process in FY05 and in FY06, $1 million 

was provided. 

In FY 2006, the 18-year lawsuit settlement was reached in September 2006, by the U.S. 

Departments of the Interior and Commerce, NRDC, and FWUA. The Settlement received 

Federal court approval in October 2006. The Settlement is based on two goals; 

to restore and maintain fish populations in “good condition” in the main stem of the San 

Joaquin River below Friant Dam to the confluence of the Merced River, including naturally 

reproducing and self-sustaining populations of salmon and other fish and to reduce or avoid 

adverse water supply impacts to all of the Friant Division long-term contractors that may result 

from the Interim Flows and Restoration Flows provided for in the Settlement. As a result the 

Settlement, a multi-agency State and Federal program, entitled the San Joaquin River 

Restoration Program, was established to carry out the terms of the agreement that would meet 

the requirements of 3406(c)1. 

FY 2006 accomplishments for the San Joaquin River include the following: 

• Integrated Information Management System (IIMS) Development - An 

interdisciplinary training workshop was held to present the work completed to date 

on the river restoration information management system proposed for the San 

Joaquin River and other river restoration activities in the MP-Region. Following the 

update, additional efforts to analyze, customize, and implement an IIMS for the 

SJRRP prior to 2009 were initiated. 

• The Milburn-Hansen Project - DWR continued their work on sediment transport 

through the study reach for the gravel pit restoration analysis. DWR made further 

progress on comparing and contrasting transport under current conditions and 

design conditions so that planners would have more information to help select the 

best alternative to construct the berm to re-isolate the Milburn gravel pit from the 

main stem San Joaquin River. 

• The Endangered Species Recovery Program (ESRP) – ESRP completed a pilot study 

to develop methodology to survey the San Joaquin River for blue elderberries 

(Sambucus mexicanus), host plant of the valley elderberry longhorn beetle (VELB;

Desmocerus californicus dimorphus), a federally listed threatened species. For 2006, a 

final report was initiated to document the results. 

• San Joaquin River Aquatic Inventory - Through an agreement with the California 

Department of Fish and Game (DFG), an inventory of the existing aquatic fauna and 

flora within the San Joaquin River between Friant Dam and the Merced River was 
CVPIA – Annual Report for Fiscal Year 2006 51 

conducted. In 2006, DFG completed their review of the major animals and plants 

within the study reaches and the water condition information that was pertinent to 

the interpretation of the inventory results. 

• San Joaquin River Water Quality Monitoring - New water temperature data was 

acquired along certain reaches of the restoration study area at the six recently 

installed monitoring sites. The 2006 data collected was incorporated into the draft 

2005 Data Summary and a 2005 and 2006 Data Summary was completed and 

distributed to the involved participants and interested public. 

• Point Reyes Bird Observatory (PRBO) - PRBO Conservation Science completed a 

three-year monitoring effort of birds and associated vegetation in riparian habitat 

between Friant Dam and the Merced River. A final report was prepared 

documenting the results, management recommendations, and included a long-term 

monitoring plan to evaluate bird communities along the river. 

• San Joaquin River 2005 and 2006 Data Collection and Study Model Development 

and Calibration - Additional San Joaquin River temperature monitoring was 

conducted at ten locations from April 2006 through July 2006. This data was used to 

further calibrate the HEC-RAS and HEC-5Q models and a summary of each process 

was completed and transmitted to the participants involved. 

• San Joaquin River Restoration Settlement Technical Support - This was the main 

effort conducted for 3406(c)1 in FY06. To assist Reclamation and Interior policy 

makers in the Settlement discussions, a technical team was established to respond to 

questions and issues related to planning, project management, contracting services, 

engineering and design, environmental compliance, and land management. The 

team prepared various scenarios (i.e. schedules/timelines) for the infrastructure 

improvements proposed for the Settlement; provided technical support on sitespecific analyses; and developed a recommendation on how the Settlement terms 

could be initiated upon approval (i.e. appoint an interim Program Manager to 

establish an interdisciplinary team to develop the Program Management Plan for 

Settlement implementation). 

Project Title: Refuge Water Supply Program – Refuge Water Conveyance 

Program Component

 CVPIA Section 3406(d)(1-5) 

FY 2006 Funding: $8,016,077 

FY 2006 Accomplishments: 

The CVPIA directs Interior to provide long-term, reliable water supplies to 19 specific wetland 

habitat areas in the Central Valley comprised of State wildlife areas, Federal wildlife refuges, 

and one private refuge (hereinafter referred to as refuges). The CVPIA authorized such water 

to be provided from CVP supplies and from water acquired through the Water Acquisition 

Program established pursuant to section 3406(b)(3). The CVPIA also authorized Interior to 

construct or acquire from non-federal entities water conveyance facilities and conveyance 

capacity as necessary for the delivery of water to the refuges. 
CVPIA – Annual Report for Fiscal Year 2006 52 

The Refuge Water Supply Program consists of four separate, but highly coordinated, 

components to provide and deliver water supplies to the identified refuges. These components 

are: 1) the Refuge Water Conveyance “Wheeling” Program component, which provides for the 

delivery of Central Valley Project water and water acquired on the open market to the refuges; 

2) the Facilities Construction Program component (a subset to the Refuge Water Conveyance 

Program), which constructs conveyance facilities necessary to obtain the needed capacity for 

delivery of water to the refuges; 3) the San Joaquin Basin Action Plan Construction Program 

component (a subset to the Refuge Water Conveyance Program), which constructs conveyance 

facilities necessary for obtaining needed capacity for delivery of water to those refuges within 

the San Joaquin Basin Action Plan lands; and 4) the Water Acquisition Program (WAP) 

component, which acquires Incremental Level 4 water on the open market from willing sellers 

for the purpose of delivery to the refuges. 

The Refuge Water Conveyance Program conveys prescribed quantities of water to the 

boundaries of the refuges through contracts and cooperative agreements with wheeling entities 

utilizing their conveyance systems. As of the end of FY 2006, ten long-term (7-50 years) 

conveyance agreements were in place and being used to deliver water to certain refuges. These 

long-term agreements are with San Luis Canal Company, aka Henry Miller Reclamation District 

(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, Glenn-Colusa Irrigation District, and the 

California Department of Water Resources (CDWR). 

FY 2006 funds were primarily expended for the conveyance of water to those CVPIA Central 

Valley identified refuges, including administration of conveyance agreements, and coordination 

for the overall Refuge Water Conveyance Program. 

Numerous biological benefits that have resulted from having a reliable, year-round water 

supply that adequately meets the delivery schedule for wetland management on CVPIA 

wildlife refuges. Habitat is now available during the months of August and early September 

which benefits early migrant waterfowl and shorebirds, and also provides habitat for resident 

wildlife and their young during a critical time of the year when wetland habitat is particularly 

limiting. 

Applying water for semi-permanent and permanent wetland habitat in the spring and summer 

directly benefits the recovery of special status species such as the giant garter snake, white-faced 

ibis, and tricolored blackbirds. Wintering wildlife also benefit because this habitat type provides 

diversity in a landscape dominated by shallow wetland habitat. 

Seasonal wetlands are now maintained and de-watered to coincide with peak migration times 

of shorebirds and waterfowl. Timely de-watering also promotes the germination and irrigation 

of important moist-soil food plants, such as swamp timothy grass and watergrass. These plants 

provide a high-energy food source through both their seeds and associated invertebrate 

communities. The increase in supply reliability allows wetland managers to lower water depths 

to make seeds and invertebrates available without the fear of having wetlands completely 

evaporate. 
CVPIA – Annual Report for Fiscal Year 2006 53 

Finally, the ability to battle avian disease outbreaks, such as botulism and cholera, is greatly 

assisted by applying additional water and creating a “flow through” system of water delivery 

and drainage. This “flow through” also helps deal with wetland areas high in salinity, which 

are often lower in productivity and diversity. CVPIA water allows wetland managers to “flush” 

salts from wetland basins and improve soil quality. 

FY 2006 accomplishments include the following: 

1. Coordination with the Interagency Refuge Water Management Team (IRWMT) to 

develop Level 2 and Incremental Level 4 water delivery schedule scenarios, expedite 

refuge monthly water delivery schedules, and prioritize limited Incremental Level 4 

water supplies 

2. Delivery of Level 2 and Incremental Level 4 quantities of water per the refuge water 

supply contracts according to the delivery schedules provided by Grassland Water 

District, U.S. Fish and Wildlife Service (FWS), and California Department of Fish and 

Game (CDFG). Based on Water Year 2005 (March 1, 2005, thru February 28, 2006), 

approximately 374,671 AF Level 2 water and approximately 81,711 AF Incremental Level 

4 water were delivered to refuge boundaries. 

3. Negotiation of a second amendment to the groundwater pumping reimbursement 

agreement with CDFG for the purpose of supplementing Level 2 surface water supplies 

up to full Level 2 allocation for the Gray Lodge Wildlife Area (GLWA). This agreement 

is expected to be extended until the Reclamation-contracted facilities construction 

project for Biggs-West Gridley Water District (BWGWD) is completed, after which 

BWGWD will have capacity to convey full Level 4 water supplies to the boundary of 

GLWA. 

4. Continued development of an integrated database for refuge water supply accounting, 

delivery scheduling, tracking and invoicing. Contract awarded on August 23, 2006, for 

Oracle programmer for purpose of completing database design. Completion of Phase I 

of database project expected by end of FY 2007. 

5. Continued support for the Load Reduction Monitoring Study at Grassland Wetlands. 

Involves wildlife studies of modified water management of Grassland Resource 

Conservation District wetlands to minimize water quality impacts to the San Joaquin 

River. These efforts have potential application for development of water quality Best 

Management Practices (BMPs) for various wildlife refuges in the San Joaquin River 

Basin. 

6. Participation with the WAP in the investigation for potential use of groundwater 

resources, including conjunctive use, to augment Incremental Level 4 supplies. 

7. Initiation of cost share development process to determine current cost share 

apportionment for the State of California related to Incremental Level 4 water supplies, 

including water acquisition, certain conveyance construction, and water deliveries costs. 

This process covers the last five fiscal years, and efforts are coordinated with FWS, 

CDFG, and California Department of Water Resources (CDWR). 
CVPIA – Annual Report for Fiscal Year 2006 54 

8. Initiation of formal negotiations on a reimbursement agreement between Reclamation 

and CDFG for reimbursement of water conveyance costs to CDFG for water deliveries to 

Mendota Wildlife Area. Agreement is expected to be executed by December 2006. 

9. Participation in the CVPIA Program Activity Report (CPAR) process, which consists of a 

review of agency implementation of CVPIA. 

10. Participation in development of the latest draft of the Mendota Wildlife Area 

Environmental Assessment/Impact Statement, which analyzes alternatives to provide 

firm year round water supplies to Mendota Wildlife Area. 

Project Title: Refuge Water Supply Program – Facilities Construction Program 

Component

 CVPIA Section 3406(d)(1-5) 

FY 2006 Funding: $664,764 

FY 2006 Accomplishments:

The Refuge Facilities Construction Program (RFC Program) is one of four components of the 

Refuge Water Supply Program, and is a subset to the Refuge Water Conveyance Program 

component. The RFC Program was developed to provide for the construction of new and/or 

improvements to existing external conveyance systems to obtain needed conveyance capacity to 

provide for the long-term reliable delivery of firm full Level 4 water supplies to the boundary of 

eight specific Federal and State wetland habitat areas (refuges) in the Central Valley. These 

refuges are the Sacramento, Delevan, Colusa, Sutter, Kern, and Pixley National Wildlife 

Refuges, and the Mendota and Gray Lodge Wildlife Areas of the State of California. 

FY 2006 accomplishments include the following: 

1. Continued development of the draft environmental assessment/initial study (EA/IS) 

documentation for conveyance of water supplies to the Mendota Wildlife Area. The 

final EA/IS is expected to be completed in FY 2008. 

2. Continued progress on the development of the Design Data Report based on data 

collection of water flows, water levels, and seepage issues of the Biggs-West Gridley 

Water District conveyance facilities. Upon completion of the Design Data Report, the 

RFC Program will move forward on design and construction of improvements to the 

facilities at Biggs-West Gridley Water District. This project will result in increasing the 

capacity of these facilities to provide for long-term reliable delivery of full Level 4 water 

supplies to the Gray Lodge Wildlife Area. The Design Data Report is expected to be 

completed in FY 2008. 

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

Program Component

 CVPIA Section 3406(d)(1-5) 

FY 2006 Funding: $2,530,000 

FY 2006 Accomplishments: 
CVPIA – Annual Report for Fiscal Year 2006 55 

The San Joaquin Basin Action Plan Construction Program (SJBAPC Program) is one of the four 

components of the Refuge Water Supply Program, and is a subset to the Refuge Water 

Conveyance Program component. The purpose of the SJBAPC Program is to modify existing 

conveyance facilities and/or construct new conveyance facilities to provide internal wetland 

habitats (refuges) infrastructure capacities for conveyance of full Level 4 water within those 

CVPIA refuges identified in the San Joaquin Basin Action Plan/Kesterson Mitigation Plan 

lands. The SJBAPC Program also provides for the construction of new and/or improvements to 

existing external conveyance systems to obtain needed conveyance capacity for the long-term 

reliable delivery of firm full Level 4 water supplies to the boundary of these refuges. The 

refuges served by this program are the San Luis, West Bear Creek, East Bear Creek, Kesterson, 

and Freitas Units of the San Luis National Wildlife Refuge Complex; Salt Slough and China 

Island Units of the North Grasslands Wildlife Area; Los Banos Wildlife Area; and the Grassland 

Resource Conservation District. 

FY 2006 accomplishments include the following: 

1. Continued progress on capacity and efficiency improvements to the O’Banion Bypass of 

the Central California Irrigation District facilities which takes water from the Outside 

Canal to the Main Canal to increase flow capacity. Project is expected to be completed in 

FY 2007. 

2. The issuance of Section 401 Water Quality Certification from the California Regional 

Water Quality Control Board and a 404 Nationwide Permit from the Corps of engineers 

for construction of Phase I of the East Bear Creek Unit of the San Luis National Wildlife 

Refuge Complex located in Los Banos, California. 

3. Continued progress on the construction of the Phase I East Bear Creek Unit conveyance 

facilities. 

4. Completed a substantial level of design and specifications for the Phase II East Bear 

Creek Unit construction project, consisting of Island C Canal Pumping Plant and San 

Joaquin River crossing. 

Project Title: Ecosystem/Water System Operations Models 

 CVPIA Section 3406(g) 

FY 2006 Funding: $550,000 

FY 2006 Accomplishments: 

The objective of the Ecosystem/Water System Operations Models program is to develop readily 

usable and broadly available models and supporting data to evaluate the ecologic and 

hydrologic effects of existing and alternative management strategies of public and private water 

facilities and systems in the Sacramento, San Joaquin, and Trinity watersheds. Specific to FY 

2006 are: 

A. CalSim III Development 

B. Completion of CalSim II San Joaquin Review & Documentation 

C. Reservoir & River Water Quality, Temperature, and Habitat Model Developments 
CVPIA – Annual Report for Fiscal Year 2006 56 

D. Training of agency and private sector staff in use of models 

E. Membership and Participation in Professional Organizations 

The Ecological/Water Systems Operations Models, CVPIA Section 3406(g) program is a 

continuing program that started in 1994. 

In previous years the program has supported the Ecosystem Modeling Consensus Project, 

review and update of the Central Valley Ground-Surface water model (CVGSM); development 

of graphical user interfaces (GUI) for PROSIM and SANJASM and their successor, ECOSIM-W 

; development of the 3-D temperature model for Whiskeytown Reservoir, development of 

CalSim II logic and hydrologic input. 

Since 1998 this program has supported a steadily increasing level of support for CalSim II 

development and application. The California Department of Water Resources (DWR) and 

Reclamation have made a large investment in 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 is used in most, if not all, current water supply improvement studies. 

This program also supports the new development of reservoir and river management models 

including water quality and biologic models used by the Division of Planning, U.S. Fish and 

Wildlife Service (USFWS) and private contractors for modeling support for operations and 

planning. 

This program supports training conducted by Reclamation and the California Department of 

Water Resources. The Mid-Pacific Region Division of Planning, the U.S. Fish and Wildlife 

Service, the California Department of Water Resources (DWR), and other stakeholders have 

been trained under funding from this program. 

This program also provides Reclamation with the opportunity to leverage the funds by 

participating in cost-sharing of development and applications of CalSim and other models. 

The primary benefit of this funding has been the development of CalSim into the reservoir 

system model of choice for investigations of managing and modifying the Central Valley Project 

and the State Water Project. CalSim was the model applied to develop the most recent Central 

Valley Project Operations Criteria and Plan (CVP OCAP). 

FY 2006 accomplishments include the following: 

1. The staff of the River Systems Analysis Branch (MP-710), Reclamation’s Technical 

Service Center, Derek Hilts (USFWS), and private contractors developed code and data, 

reviewed CalSim II, and participated in CalSim III development. 

2. Support of a comprehensive review of the CalSim II simulation of salinity at Vernalis on 

the San Joaquin River; and improved simulation of the east side reservoir operations and 

irrigations demands. This review has received an additional $80,000 of support from the 

California Water and Environmental Modeling Forum, Calfed Science and water 

districts. This activity is unprecedented in that Reclamation simultaneously publicly 
CVPIA – Annual Report for Fiscal Year 2006 57 

introduced these model enhancements and initiated an outside review in a meeting in 

Modesto (August 2005). Reclamation will release the results of the peer review and its 

responses to issues raised in early 2007. 

3. In cooperation with California DWR, Reclamation has begun significant improvements 

for the new CalSim III model including improved methods for evaluating hydrologic 

inputs based on DWR’s Integrated Flow Model (IWFM), groundwater simulation 

capability based on the new California Central Valley Simulation model (C2VSIM), and 

a revised water quality simulation for the San Joaquin River. CalSim III will include a 

consistent implementation of hydrology and groundwater in both the Sacramento and 

San Joaquin Valley. These activities will be completed during FY 2007. 

Project Title: Land Retirement Program

 CVPIA Section 3408(h) 

FY 2005 Funding: $1,494,552 

FY 2005 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 to: 

1. Improve water conservation by district, or improve the quality of an irrigation district’s 

agricultural wastewater. 

2. Reduce drainage and improve water quality in the San Joaquin River, and to use retired 

lands to create additional wildlife habitat in the San Joaquin Valley. 

FY 2005 accomplishments include the following: 

Acquisition 

Land acquisition at Atwell Island is focused on the inclusions within the already acquired acres. 

Letters were sent to all landowners of record for parcels within the Atwell Island Water District 

in either Tulare or Kings Counties. Approximately 38 acres have accepted offers and 20 acres 

have offers pending. An appraisal has been requested for a 193-acre parcel. Land acquisitions 

at both the Tranquillity and Atwell Island Project Sites have to date resulted in 9,055 acres being 

acquired. Of those lands, 8,345 acres are retired from irrigated agriculture or have reduced 

drainage. 

Monitoring and Reporting

Groundwater and soil monitoring continued at the Tranquility and Atwell Island 

Demonstration Project sites. Performance Standards for the biological opinion were met for 

physical parameters, with the exception of groundwater quality, which was highly saline 

with high concentrations of selenium. The bio-availability of the selenium was extremely 

low, however, due to the increased depth from surface to groundwater. At Atwell Island 

site were assessed by BLM for vegetation structure and small mammal populations. 
CVPIA – Annual Report for Fiscal Year 2006 58 

Complete restoration to upland habitats found in the San Joaquin Valley could take many 

years to achieve, but the program’s work has restored portions of the land and continues to 

adapt techniques to achieve desired habitat values. Selenium toxicity to wildlife was a 

concern on drainage impaired farmlands retired from irrigated agriculture in the San 

Joaquin Valley. Water, soil, and biota are being monitored on LRDP lands to comply with 

the Fish & Wildlife Service Biological Opinion requirements. 

The website contains ancillary trials results developed by ESRP. Links are provided to the 

annual reports and the 5-year report fro Tranquillity. Monitoring results are used to inform 

decisions regarding large scale land retirement, as a means to address agricultural drainage 

problems in the San Joaquin Valley. 

Restoration 

In FY 2006 at Atwell Island, BLM performed restoration activities on 431 acres. Restoration 

actions included: 225 acres burned and seeded with natives; 2 acres of sacaton grass plugs; 40 

acres wildlife crops; 50 acres interplanting with Isocoma; 14 acres of seeding on a sump with 

iodine bush and suaeda seed; 20 acres shrub seeding; 10 acres of disking and native seed; and 70 

acres of agricultural flaming and seeding. Sites are currently being monitored by BLM to 

determine the long-term success of these and previous years’ plantings. The prolonged rainy 

season in 2006 produced prominent floral displays. 

Evaluation of upland habitat restoration techniques is ongoing at both sites. No one “recipe” will 

fit all soil types or be successful in a given rainfall year. Many variables are being evaluated and 

recommendations being formulated. Successes at the Atwell Island site are being adapted to 

future plantings. Monitoring of these efforts contributes to this adaptability. 

During Atwell Island wildlife surveys of sensitive plants and animals BLM observers found: a 

population of the endangered Tipton’s Kangaroo Rat; a breeding population of sensitive 

Burrowing Owls; a breeding population of sensitive Coast Horned Lizards; a population of the 

sensitive San Joaquin Valley Coachwhips; a breeding population of Swainson’s Hawks; and a 

population of a sensitive plant, Hoover’s Woolystar. The wildlife sighting database now 

contains over 9500 observations. BLM developed plant and animal lists and a photo-illustrated 

flora for the Atwell Island project area. The plant list now contains 135 species from 43 families. 

The animal list includes 185 bird, 22 mammal, 9 reptile, 4 amphibian, and 23 butterfly species. A 

photo-illustrated flora of Atwell Island was developed by BLM. 

Site management at Tranquillity by ESRP focused on maintenance of the 100 native plant 

nursery facility. Site preparation, pre-planting weed control, planting; construction of 

exclosures and ongoing weeding, seed collection, and mowing were activities performed. The 

seed cleaning for 2005 harvest was completed. The 2006 harvest is being dried and stored. A 

series of illustrated “manuals” regarding proper use of the equipment and seed cleaning 

protocols for different native plant species continues to be developed. ESRP provided 1,750 

pounds of native seed from the facility that were planted in two wildlife units in partnership 

with the Westside RCD. Sheep grazing continued as a way to control weeds and reduce fire 

damage. Two restoration trials/demonstrations were installed at Tranquillity in collaboration 

with Dr. Ken Lair of TSC. 
CVPIA – Annual Report for Fiscal Year 2006 59 

Partnerships and Outreach 

Critical to the success of the restoration activities at Atwell Island is the partnership BLM has 

with cooperating farmers to. Other efforts by BLM and FWS centered on the continued efforts 

with the Tulare Lake Basin Working Group and the continued help provided to develop the 

Tulare Basin Wildlife Partners as an NGO. This NGO began to operate as a “Friends Group” to 

the Atwell Island Project. BLM continued coordination via partnerships with other NGOs and 

agencies that included the Tulare County Audubon Society; Alpaugh School District; Citizens 

for a Better Alpaugh; State Park Service – Allensworth SHM; USDA NRCS; USDA Forest 

Service (Trails Unlimited); and the Kern NWR.

DISCUSSION OF CVPIA IMPLEMENTATION AND RESULTS 

Reclamation and the Service have attempted to implement, in a purposeful, proactive manner, 

the fish and wildlife provisions of the Act believed to be the most important, most urgent, or 

that would result in the greatest or most immediate contribution to attainment of its three 

primary fish and wildlife restoration goals: (1) sustainable doubling the natural production of 

anadromous fish, (2) providing water to refuges, and (3) mitigating for other CVP impacts. 

Measuring progress towards attaining the goals and objectives of CVPIA 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 2006 as it has been for any of 

the prior 14 years of CVPIA implementation. 

Nevertheless, we believe target fish and wildlife resources are responding to CVPIA measures. 

Implementation of long-term CVPIA programs and plans appears to be gradually realizing its 

goals and objectives: the number of salmon returning to the Central Valley is increasing, 

spawning in areas where they have not been seen for many years; hundreds of thousands of 

ducks, geese and other migratory birds are using wetland areas newly created or greatly 

enhanced under the Act; avail diseases are declining throughout the valley; tens of thousands of 

acres of habitat have been acquired to protect threatened and endangered species; and 

thousands of acres have been restored and/or enhanced to benefit 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 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, Spawning Gravel Replenishment Program, AFRP, and AFSP. 

For the Clear Creek Restoration and Spawning Gravel Replenishment programs, draft 

documents have been produced that detail objectives, outcomes, and progress. The Restoration 
CVPIA – Annual Report for Fiscal Year 2006 60 

Fund Roundtable has provided feedback, and the documents are continually improving. 

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 Service, 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 use the 

information to develop screening criteria to minimize diversion impacts. 

Anadromous Fish - Biological Response 

Chinook salmon continue to be a high priority for CVPIA restoration efforts. A majority of 

implemented measures and the $498.4 million obligated over the past 14 years has been focused 

on this species. While the overall number of salmon along the West coast has declined, adult 

returns to the Central Valley and catch off the California coast have increased, correlating well 

with implementation of the CVPIA, which began in 1993. While other factors such as 

hydrology, ocean conditions, and fishing regulations have undoubtedly contributed to these 

increases, the declining West coast salmon fishery has also been subject to these factors and 

shows a different population trend. 

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. 

 

The fall-run Chinook salmon population in Clear Creek has increased greatly following 

implementation of these measures. Spawning production of fall-run Chinook salmon in Clear 
CVPIA – Annual Report for Fiscal Year 2006 61 

Creek, which averaged 3,600 fish during 1967-1991, increased to an average of 12,313 fish 

during 1992-2006. 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 

sustained increases in numbers of these special status species, and whether 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. 

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 salmon returns 

have been steadily improving. Natural production of Butte Creek Chinook salmon, which 

averaged only 1,800 fish during 1967-1991, increased to an average of 14,000 fish during 1992–

2005 (Table 2). 

In some years, natural production of salmon on several Central Valley streams has reached or 

exceeded population numbers set by the Anadromous Fish Restoration Plan (USFWS 2001) 

(numeric doubling goals), but has not yet been determined to be sustatinable as required by the 

CVPIA. To determine if increased natural production is sustainable on a long-term basis, 

several life cycles (three to five years per cycle) of continued monitoring is necessary under a 

variety of environmental conditions (USFWS 1995a:2-IX-5-18). A statistical process is being 

developed to assist in determining the sustainability of increased population levels. 

Conversely, there are many other streams where the production of salmon and other 

anadromous fish have declined (e.g., Table 2). 

In Central Valley rivers and streams with sufficient data, Table 2 presents natural production of 

Chinook salmon for the period of CVPIA implementation (1992-2006), as a percentage relative 

to the 1967-1991 baseline. 

For example, Table 2 shows natural production of Clear Creek fall-run Chinook salmon to be 

248 percent greater than the baseline period. If Clear Creek fall-run Chinook salmon numbers 

were shown to be sustainable, the anadromous fish doubling goal for this run on Clear Creek 

could have been exceeded by 148 percent. 

In contrast, production for Yuba River fall-run Chinook salmon in Table 2 is 22 percent above 

the baseline, or 78 percent below the numeric doubling goal and production for Tuolumne 

River fall-run is 50 percent below the baseline or 150 percent below the numeric doubling goal. 

Several small streams and two rivers identified in the AFRP Restoration Plan (Cow, Paynes, 

and Antelope creeks; miscellaneous small creeks, and Bear and Calaveras rivers) have 

insufficient data to make a determination regarding their anadromous fish production status 

relative to the baseline period. 

Four of the 27 Chinook salmon populations in Table 2 have exceeded their CVPIA numeric 

doubling goals, and 8 populations, including these 4, have exceeded baseline 1967-1991 

production (Table 2). As stated earlier, to determine progress toward anadromous fish 

doubling goals (as opposed to just numeric doubling goals), will require continued monitoring 

to determine if these production levels are sustainable on a long-term basis. 
CVPIA – Annual Report for Fiscal Year 2006 62 

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 agricultural fields 

containing waste grain during winter provided new seasonal habitats for waterfowl. 

Waterfowl, shorebirds, and other wetland-dependent wildlife benefited from expansion and 

enhancement of habitat. Central 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, and refuge 

managers with the ability to manage a much more diverse mix of habitat types that more fully 

satisfied year-round biological needs of many wildlife species. Prior to CVPIA, refuge 

managers had to concentrate the vast majority of water use in fall and early winter months, 

when Central Valley waterfowl numbers peaked. With passage of CVPIA, the habitat calendar 

was expanded to the full year. Under CVPIA programs, moist soil food plant irrigations are 

carried out, water is made available during August and September to satisfy needs of the first 

wintering ducks and geese that arrive in the Central Valley, maintenance flows are applied 

throughout the winter months to improve water quality and decrease the intensity of avian 

disease outbreaks, and spring and summer water provides critical nesting habitat for waterfowl 

and colonial birds. 

 

Water availability also enhances refuge managers’ ability to provide a food supply for 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 1991-1992 to an average of 26,000 acres during 1993-2006. In that same time 

period, per acre plant biomass doubled. 

Waterfowl use increased nearly as much. With more wetland habitat available in August and 

September, early fall waterfowl use in the Grassland RCD 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 alleviate waterfowl 

overcrowding, particularly in the Sacramento Valley. Waterfowl disease-related mortality, 

usually caused by overcrowding and stagnant water, decreased markedly in the Sacramento 

Valley, as birds took advantage of increased habitat and improved water quality. Cholera 

outbreaks, once frequent and widespread in the Sacramento Valley, have been reduced to only 

one major incident since passage of CVPIA. Similarly, the Sacramento NWR complex reported 

a nearly 89 percent decline in botulism since 1992, compared to the decade prior to availability 

of CVPIA water supplies and the year-around reliability they provide. 

Species other than waterfowl also benefited from CVPIA water. Sacramento Valley refuges 

reported an increased presence of western pond turtles and colonial nesting birds, such as the 

tricolored blackbird. In fact, the largest tricolored blackbird colony documented in California in 

2004 occurred at Delevan NWR, where a combined population of adults and young totalled an 
CVPIA – Annual Report for Fiscal Year 2006 63 

astonishing 230,000 . In 2006, the tri-colored population at Delevan was a smaller, but still 

substantial and thriving colony of some 40,000 individuals. In addition, refuges in the San 

Joaquin Valley noted increases in populations of giant garter snakes; nesting western, Clark’s, 

and eared grebes; black-crowned night herons; and tricolored blackbirds. Valley-wide, 

shorebird use on shallow wetlands increased by hundreds of thousands, as sandpipers, dunlins, 

yellowlegs, phalaropes, and dowitchers responded to the increased wetland availability and 

related blooms of 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 reliable, 

year-round 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 

numbers of frogs, snails, aquatic insects, and small fish. This, in turn, provided ibis with habitat 

for late-spring and summer nesting, essential components for these species. 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 in 2005. Kern NWR had a similar experience, with 50 ibis 

in 1991, 5,000 in 2001, and over 5,700 in 2006. Pixley NWR supported 200 wintering sandhill 

cranes in 1992 when the CVPIA was passed. It received its first allocation of CVPIA water in 

1993 and provided wintering habitat for more than 2,000 sandhill cranes that year. By 2001, the 

population rose to 5,100 sandhill cranes and has remained high ever since, totaling 5,800 in 

2006. 

Other Fish and Wildlife - Accomplishments

Efforts under the CVPIA to protect and provide habitat for fish and wildlife other than 

anadromous fish and wetland-dependent wildlife include fee title and conservation easement 

acquisition of almost 99,000 acres from willing sellers at fair market prices; restoration of over 

1,100 acres of native habitat for special status species; and research, surveys, and planning 

activities that contribute to recovery of CVP impacted species. These actions were 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 had been developed. 

Since 1993, 10,283 acres of drainage impaired agricultural lands have been retired from irrigated 

agriculture. Upland habitat restoration has occurred on over 2,700 acres. 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 populations 

of species associated with these habitats, and particularly those that are threatened or 

endangered, will increase substantially. 

The CVPIA Land Retirement Program Demonstration Project is indicative of the benefits that 

we expect to achieve. Monitoring results from the Fresno County site indicate a decline in the 

shallow groundwater table in response to land retirement, which is important, as the highly 
CVPIA – Annual Report for Fiscal Year 2006 64 

saline groundwater has high concentrations of selenium and boron. Restoration of these retired 

lands and their use by wildlife has not resulted in increased levels of bio-accumulated selenium 

in any of the plants, invertebrates or mammals measured. All selenium levels measured are 

considered below concentrations of concern to Environmental Protection Agency and the 

Service. 

Treating these lands has increased abundance and diversity of wildlife. Increased numbers of 

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. Populations of small mammals increased 

substantially on retired lands. Special status mammalian species observed on restored land at 

Atwell Island, including the San Joaquin kit fox and Tipton’s Kangaroo Rat, were observed 

using established hedgerows and retired lands. Adequate native seed supplies necessary for 

successful restoration are being propagated. Utilizing native plant species for upland habitat 

restoration has many challenges, primarily large weed load control. Irrigation in the first year 

has helped establish natives at Atwell Island. After one year, no further irrigation was 

necessary and the resulting vegetation was low maintenance. Knowledge of the sensitive 

species habitat needs enables proper planning and planting of required vegetation for their 

desired structure and density. 

The five year results of the Land Retirement Demonstration Project can assist in implementation 

of any large-scale San Joaquin Valley land retirement. The restoration technology learned on 

the sites can be applied to other retired lands and assist in sensitive species recovery. The 

Native Plant Nursery needs to be maintained, as the plants grown there are limited in 

occurrence throughout the San Joaquin Valley. The partnerships developed during the life of 

the program will encourage the extension of monitoring and restoration accomplishments. 

CONCLUSIONS 

Quantifiable Progress in 2006

In the first decade since the CVPIA was enacted, a vast amount of “foundation work” has taken 

place. Foundation work is essential to the final outcome, but often not highly visible. It 

involves many activities, such as data collection, research, development of alternative actions, 

alternatives analysis, feasibility studies, permitting, and design work. Adequate foundation 

work is critical if the desired outcomes of the CVPIA’s are to be achieved, including (1) fish and 

wildlife protection, habitat restoration and enhancement; (2) addressing CVP impacts; (3) 

improving CVP operational flexibility; (4) expanding water transfers; (5) protecting the BayDelta; and (6) achieving a reasonable balance of CVP water uses. Much of that work has been 

accomplished, although more must continue. 

In 2006, some significant “on the ground” achievements were made toward the overall 

environmental goals of the CVPIA. A few examples of these achievements are the restoration of 

about 431 acres of vernal pool and vernal pool-alkali meadow complex habitats on the 

Sacramento National Wildlife Refuge, placement of 6,000 tons of spawning gravel below 

Keswick Dam for spring-run Chinook salmon and steelhead on the Sacramento River, 
CVPIA – Annual Report for Fiscal Year 2006 65 

placement of 2,700 tons of spawning gravel on Clear Creek, and placement of 1,500 tons of 

spawning gravel in Goodwin canyon on the Stanislaus River to increase Chinook salmon 

spawning density. These 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. 

At the conclusion of 2006, significant progress has been made in meeting the CVPIA’s fish and 

wildlife goals. To be sure, there is much more work to be accomplished. Challenges for 

anadromous fish restoration are particularly complex on rivers where the largest, most 

important dams prevent migration to historic headwater habitats. Even so, some improvements 

appear significant. One of the most significant events through 2006 has been the increase of 

anadromous fish populations in four different Central Valley tributary streams (Table 2). Most 

notable is Butte Creek Chinook salmon (all runs); whose population has increased to an 

astonishing 750 percent of its average 1967-1991 natural production (Table 2). Such increases 

need to be sustainable to meet the CVPIA’s mandated Central Valley-wide anadromous fish 

doubling goal, 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, natural 

production of all runs of Chinook salmon has increased to 342 percent of its average 1967-1991 

natural production (Table 2). In Clear Creek, fall-run Chinook salmon natural production has 

increased to 248 percent of its average 1967-1991 production (Table 2). Chinook salmon 

populations in the American River (fall-run) and Mokelumne River (fall-run) also show 

promising trends. 

Actions taken under the CVPIA and other restoration programs, such as CALFED, are believed 

to have greatly influenced the increasing population trends for anadromous fish in widely 

dispersed areas of the Central Valley. Actions have included removal of smaller old dams and 

barriers, reopening many miles of spawning habitat; carefully planned deposition of gravel, 

recreating lost spawning habitat; improvement of riparian and floodplain habitat; better 

management of available instream water supplies; addition of fish screens at many diversions, 

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 become an essential and highly effective tool to improve 

anadromous fish populations on many streams. Approximately 11,000 tons of gravel were 

placed in the Upper Sacramento and the Stanislaus rivers, and Clear Creek in 2006. Salmon use 

of the new spawning gravels is helping to increase fish numbers in those streams. In some 

streams, deeper pools that shelter predator species have been re-configured to eliminate this 

threat to anadromous salmonid fry. 

Important achievements were also made as a result of the refuge water supply program, 

keystone in efforts to reinvigorate and expand imperiled bird, fish and animal populations in 

the Central Valley. Vital water supplies are provided to refuges in the Central Valley of 

California, known as Level 4, to meet optimum habitat management requirements. The Level 4 

water supplies consist of "Level 2" water which is usually provided by CVP project yield, and 

"Incremental Level 4" water acquired through purchase from willing sellers. 
CVPIA – Annual Report for Fiscal Year 2006 66 

In 2006, approximately 84,000 acre feet of Incremental Level 4 water supplies were acquired to 

allow optimum management on the refuges relating to increased habitat diversity, seasonal 

availability of habitat, and waterbird breeding, nesting and foraging areas. These water 

supplies provide critical wetland habitat supporting resident and migratory waterfowl, 

threatened and endangered species, and wetland dependent biota. The increased water 

supplies have expanded refuge wetland habitat and resulted in larger and healthier bird 

populations. The direct result of these acquisitions continues to be a much larger, healthier bird 

populations. 

Other types of habitat restoration also achieved significant progress in 2006. 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

Reclamation and the Service are actively assessing and rating CVPIA programs to better 

identify and improve our performance in achieving the results of the CVPIA. More specifically, 

Reclamation and the Service are assessing our overall program effectiveness, spanning from 

how well a program is designed to how well it is implemented and what results it has and will 

achieve. This review will help identify a program’s strengths and weaknesses, and will assist in 

funding and management decisions to further improve program and overall CVPIA 

effectiveness. All factors that may affect and reflect program performance will be assessed; for 

example, program purpose and design, performance measurement, evaluations, strategic 

planning, program management, and program results. This effort will further Reclamation and 

the Service’s goal of completing fish, wildlife, and habitat mitigation and restoration actions 

mandated by the Act. 

Interior is proud of its many achievements in the protection, restoration, and enhancement of 

fish and wildlife associated with the CVPIA. There is still much to be done to accomplish the 

many provisions of the CVPIA; however, Interior remains resolute in its implementation effort 

and dedicated to the accomplishment of CVPIA mandates. 

REFERENCES 

CALFED. 2000. Programmatic Record of Decision (ROD). CALFED Ecosystem Restoration 

Program. August 28, 2000. 

CALFED. 2000. Conservation Agreement Regarding Multi-Species Conservation Strategy. 

CALFED Ecosystem Restoration Program. August 28, 2000. 

CDFG. 2005. Grand Tab. California Department of Fish and Game, Native Anadromous Fish 

and Watershed Branch, Stockton, CA. February 3, 2005. 
CVPIA – Annual Report for Fiscal Year 2006 67 

USFWS. 1995a. Working paper on restoration needs habitat restoration actions to double 

natural production of anadromous fish in the Central Valley of California. Volume 2. 

U.S. Fish and Wildlife Service, Stockton, Anadromous Fish Restoration Program, CA. 

USFWS. 1995b. Working paper on restoration needs, habitat restoration actions to double 

natural production of anadromous fish in the Central Valley of California. Volume 3. 

U.S. Fish and Wildlife Service, Stockton, Anadromous Fish Restoration Program, CA. 

USFWS. 2000. Draft Biological Opinion on the Operation of the Central Valley Project and 

Implementation of the CVPIA. U.S. Fish and Wildlife Service, Sacramento Fish and 

Wildlife Office, Sacramento, CA. 

 

USFWS. 2001. Final restoration plan for the Anadromous Fish Restoration Program, a plan to 

increase natural production of anadromous fish in the Central Valley of California. 

Anadromous Fish Restoration Program, U.S. Fish and Wildlife Service, Stockton, CA.