U.S. Department of the Interior

Bureau of Reclamation 

U.S. Fish and Wildlife Service August 2012

Central Valley Project 

Improvement Act

Public Law 102-575

Annual Report

Fiscal Year 2011
Cover photographs:

Top: Contra Costa Fish Screen. Photo courtesy of USBR.

Middle: American bittern, Sacramento National Wildlife Refuge. Photo courtesy of U.S. 

Fish and Wildlife Service.

Bottom: Cottonwood Creek Anderson-Cottonwood irrigation District Siphon, posttreatment. Photo courtesy of U.S. Fish and Wildlife Service.
TABLE OF CONTENTS i

Central Valley Project Improvemen

Table of Contents
ii CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Table of Contents

EXECUTIVE SUMMARY.......................................................................................................................................ES-2

CHAPTER 1 - INTRODUCTION .................................................................................................................................1

CHAPTER 2 - FISHERIES RESOURCE AREA (3406) ............................................................................................17

(b)(1) Anadromous Fish Restoration Program.....................................................................................................18

(b)(1) “Other” & (b)(23) Trinity River Restoration Program ..................................................................................27

(b)(2) Dedicated 800,000 acre-feet Project Yield.................................................................................................31

(b)(3) & (g) Water Acquisition Program – Instream Water ...................................................................................34

(b)(4) Tracy (Jones) Pumping Plant Program......................................................................................................36

(b)(5) Contra Costa Canal Pumping Plant...........................................................................................................38

(b)(10) Red Bluff Diversion Dam..........................................................................................................................40

(b)(12) Clear Creek Restoration Program............................................................................................................43

(b)(13) Spawning and Rearing Habitat Restoration Program..............................................................................46

(b)(16) Comprehensive Assessment and Monitoring Program............................................................................49

(b)(21) Anadromous Fish Screen Program..........................................................................................................51

(c)(1) San Joaquin River Restoration Program....................................................................................................53

(g) Ecosystem and Water Systems Operations Models ......................................................................................56

CHAPTER 3 - CVP WATER OPERATIONS RESOURCE AREA (3406)..................................................................59

(b)(1)(B) Modified CVP Operations......................................................................................................................60

(b)(9) & (19) Flow Fluctuations and Reservoir Storage .......................................................................................61

CHAPTER 4 - REFUGES RESOURCE AREA (3406)..............................................................................................63

(b)(3), (d)(1), (2) & (5) Refuge Water Supply Program .......................................................................................64

(b)(3) and (d)(2) Refuge Water Acquisition..........................................................................................................67

(d)(1), (2) and (5) Refuge Water Conveyance .....................................................................................................69

(d)(5) Refuge Facilities Construction Actions.......................................................................................................72

CHAPTER 5 - OTHER RESOURCE AREA (3406, 3408, 3404, AND 3405)............................................................75

3406 (b)(1) Other Habitat Restoration Program ..................................................................................................76

3408 (h) Land Retirement Program.....................................................................................................................78

3404 (c) and 3405 Contract Renewals and Water Transfers...............................................................................80

APPENDICES

Appendix A: Progress to Date Toward CVPIA Performance Goals ....................................................................82

Appendix B: Acronyms........................................................................................................................................86

Appendix C: Glossary of Terms ..........................................................................................................................87

Appendix D: CVPIA Title 34 of Public Law 102-575 ...........................................................................................90

LIST OF FIGURES

Figure ES-1: Ongoing Programs by Resource Area and Completed Programs.............................................ES-4

Figure ES-2: FY 2011 Financial Obligations By Action Category .................................................................ES-11

Figure ES-3: FY 2011 Financial Obligations By Fund Source ......................................................................ES-11

Figure 1: Central Valley Project (CVP) System ....................................................................................................3

Figure 2: Ongoing Programs by Resource Area and Completed Programs.........................................................5

Figure 3: Program Financial Obligations By Action Category to Date ..................................................................8

Figure 4: Program Financial Obligations By Fund Source to Date.......................................................................8

Figure 5: FY 2011 Financial Obligations By Action Category .............................................................................10

Figure 6: FY 2011 Financial Obligations By Fund Source ..................................................................................10

Figure 7. Central Valley Refuges Receiving CVPIA Water Supplies ..................................................................66
TABLE OF CONTENTS iii

LIST OF TABLES

Table ES-1: FY 2011 Funding Obligations by Program Activity (rounded) ...................................................ES-10

Table 1: FY 2011 Funding Obligations by Program Activity (rounded) .........................................................11

Table 2: Yearly Estimates of Natural Production of Anadromous Fish and the Average Natural

Production by Species within Central Valley River and Streams, 1992-2010.................................19

Table 3: Summary of Progress Towards Completing 289 Final Restoration Plan Actions and 

 Evaluations by Watershed, FY 1992-2011......................................................................................20

Table 4: Summary of Progress Towards 128 High and Medium Priority Actions Final Restoration 

 Plan with End Points (53 Structural, 75 Non-Structural), FY 2011 and 1992-2011.........................21

Table 5: Average Natural Production of Anadromous Fish in Each Watershed Compared to the 

Anadromous Fish Restoration Program Doubling Goal Targets, 1992-2010..................................22

Table 6: FY 2010 Salmonid Production, Natural vs. Hatchery .....................................................................28

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2011...............................................29

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2011 .................................29

Table 9: Rehabilitation Site Construction Summary, 2005-2011 ..................................................................30

Table 10: Allocation Target and Use of (b)(2) Water, 2001-2011 ....................................................................32

Table 11: FY 2011 Use of (b)(2) Water by Location........................................................................................32

Table 12: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 1994-2011............35

Table 13: Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan Actions...........37

Table 14: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2011...................................48

Table 15: AFSP Projects by Watershed and Cubic Feet per Second (cfs) Screened, 1994-2011..................52

Table 16: Ecosystem and Water System Operations Models That are Developed by 3406(g) Program .......57

Table 17: arryover Storage at Shasta and Trinity Reservoirs, 1998-2011 ......................................................62

Table 18: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2011...........................................................68

Table 19: Level 2 (L2), Incremental Level 4 (Inc L4) and Full Level 4 Delivery Water by Year, 2002-2011....70

Table 20: Water Targets and Deliveries for Each Refuge (FY 2011) ..............................................................71

Table 21: Target Level 4 Conveyance Capacity vs. Actual by Refuge............................................................74

Table 22: Acres of Habitat Protected and Restored, 1996-2011.....................................................................77

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2011..................................79

EXECUTIVE SUMMARY ES-

Central Valley Project Improvemen

Executive Summary
ES-2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

PURPOSE

This fiscal year (FY) 2011 CVPIA Annual

Accomplishments Report summarizes the actions 

authorized under the Central Valley Project 

Improvement Act (CVPIA or Act) of 1992 an

highlights FY 2011 accomplishments (October 1, 

2010 - September 30, 2011). Section 3408 (f) of 

the Act directs the Secretary of Interior to submit

an annual report describing all significant actions 

taken toward achievement of the intent and purposes 

of Title 34. Goals of the Act, CVPIA background,

program funding and recent developments are 

presented in the Introduction in Chapter 1. Program

performance measures, 2011 accomplishments, and 

funding obligations for Sections 3404, 3405, 3406 

and 3408 CVPIA Program activities are presented in

Chapters 2, 3, 4, and 5 by resource area (Fisheries, 

Water Operations, Refuges, and Other Resources). 

Appendix A shows the current Programs and their 

status toward completion of goals. The relevant 

Sections of the Act are provided for reference in 

Appendix D. 

BACKGROUND

Central Valley Project Improvement 

Act of 1992

On October 30, 1992, Public Law 102-575, the 

Reclamation Projects Authorization and Adjustment 

Act of 1992, was signed into law by the President. 

This legislation included Title 34, the Central Valley 

Project Improvement Act (CVPIA or Act)  The CVP

amends previous authorizations of the CVP to include 

fish and wildlife protection, restoration, and mitigation 

as project purposes having equal priority with 

irrigation and domestic uses, and fish and wildlife 

enhancement as a project purpose equal to power 

generation. The Department of the Interior, Bureau

of Reclamation (Reclamation) and Fish and Wildlife 

Service (Service), in collaboration with State and local 

governments, Tribes, non-governmental organizations, 

and stakeholders, implement activities to meet the 

Act’s purposes. The CVPIA also contributes to the

State’s interim and long-term efforts to protect the San 

Francisco Bay/Sacramento-San Joaquin River Delta 

Estuary. 

2011 Water Year

The Water Year type is a designation that is based 

on hydrologic indices for the Sacramento and San 

Joaquin Valleys. Water Year type is either wet, above 

Executive Summary

Mallard at Gray Lodge WA
EXECUTIVE SUMMARY ES-

normal, below normal, dry or critical. Water year 

type is determined by precipitation and is therefore 

indicative of local and regional conditions that 

influence climate, snowpack and runoff. Water Year 

2011 was classified as a wet year and when coupled 

with the above normal year in 2010, the abundance 

of water was a relief to the drought experienced from 

2007 through 2009. 

CVPIA Programs have seen varying effects from

the hydrology of 2010 and 2011. Biologically, the 

increased flows benefited aquatic species. For 

example, increases in outflow from the delta serve to 

trigger the migration of fish upstream. Preliminary, 

Chinook salmon returns through Central Valley 

streams appear to be on a positive, increasing trend 

since 2010.

However, the same water was a benefit to fish had 

minor negative effects to construction projects. Heavy 

rains encountered in November/December 2010 

and high flows in March 2011 flooded the work area 

and slowed construction at the Red Bluff Fish Passage 

Improvement Project

Overall and looking forward, this improved water 

condition is encouraging for the 2012 Water Year 

since the CVP will enter the next water year with 

improved reservoir carryover storage.

CVPIA GOALS AND FY 2011 

ACCOMPLISHMENTS

The current focus of the CVPIA Program is on fish

and wildlife restoration, water management, and 

conservation activities, authorized in Sections 3406 

and 3408 of the Act. Additionally, Sections 3404 

and 3405 focus on water transfers and contract 

renewals, and the management of these activities are 

related to the resource goals. These goals fit within 

four broad resource areas: fisheries, water operations, 

refuges and other. Figure ES-1 shows the active 

CVPIA programs that contribute to each resource

area as well as those provisions that are complete or 

inactive. 

Presented below are the Program goals by resource 

area along with 2011 accomplishments. These 

summaries offer a snapshot of the work accomplished 

in FY 2011. Chapters 2, 3, 4 and 5 of this report 

provide more information on the accomplishments of 

each program. 

A synopsis of the programs targets, status to date and 

2011 accomplishments are presented in Appendix A.

Two ongoing programs, Flow Standards and 

Objectives and Short Pulse Flows, are incorporated 

into the operations of overarching programs such as 

Cleark Creek and Flow Fluctuations.

Fisheries Resource Area Goals

Central Valley

The Act directs Interior to, “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 target established by 

this section of the Act is known as the “fish-doubling 

goal”, which pertains to Chinook salmon, rainbow 

trout (steelhead), striped bass, American shad, white 

sturgeon and green sturgeon; species believed 

to have been impacted by CVP construction and 

operation. Further, the AFRP’s 2001 Final Restoration 

Plan (Plan) identified 289 actions and evaluations that 

were determined to be reasonable given numerous 

technical, legal and implementation considerations. 

When the Plan’s actions are implemented in concert, 

they provide for comprehensive restoration that 

improves freshwater habitat for Chinook salmon and 

other anadromous fish species. 

In addition to the anadromous fish “doubling goal”,

the CVPIA Program uses the suite of structural and

non-structural restoration actions from the Plan 

to measure progress. For example, at Red Bluff 

Diversion Dam, a new fish screen and pumping 

plant will be constructed. On Clear Creek, channel 

rehabilitation projects are occurring. And within 

the Sacramento, Stanislaus and American rivers, 

spawning gravel is being placed. These actions, 

through various fisheries programs, all contribute to 

the reasonable efforts identified to ensure sustainable 

natural production of anadromous fish within the 

Central Valley rivers and streams.
ES-4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

While the fisheries programs are currently 

administered individually, the Science Based 

Management Framework approach discussed below 

under Recent Developments aims to coordinate, 

integrate and prioritize CVPIA efforts across

geographic areas. 

2011 Accomplishments

Anadromous Fish Restoration Program 

(AFRP), 3406 (b)(1)

Sacramento Basin

The AFRP construction projects conducted in the 

Sacramento basin in 2011 included a riverine 

enhancement on the American River; an Antelope 

Creek project to improve passage to 13 miles of 

spawning and holding habitat; and a fish screen and 

ladder project at the Eagle Canyon site. 

The AFRP collected data and conducted habitat 

assessments on various riverine systems in the 

Sacramento basin in 2011. A temperature 

assessment report was conducted on Dry Creek, a 

tributary to Bear River; surveys were conducted on 

Cottonwood Creek for the Nonnative Invasive Plant

Management and Control Project; flow and turbidity 

data were collected for the Cottonwood Creek 

Geomorphological Analysis Project; habitat surveys 

above a barrier in Cow Creek were completed 

for fall-run Chinook and steelhead, and design 

alternatives were developed with stakeholders; 

monitoring activities and reports for the green 

sturgeon were conducted on the Feather and Yuba 

Figure ES-1: Ongoing Programs by Resource Area and Completed Programs

Ongoing Programs Completed Programs

Fisheries Resources

Central Valley

3406 (b)(1) Anadromous Fish 

Restoration Program

3406(b)(2) Dedicated Project Yield

3406(b)(3) Instream Water Acquisition 

Program

3406 (b)(4) Tracy Pumping Plant 

Program

3406 (b)(10) Red Bluff Diversion Dam

3406 (b)(12) Clear Creek Restoration 

Program

3406 (b)(13) Spawning and Rearing 

Habitat Restoration Program

3406 (b)(15) Head of Old River 

Barrier

3406 (b)(16) Comprehensive 

Assessment and Monitoring Program

3406 (b)(21) Anadromous Fish 

Screen Program

3406 (g) Ecosystem and Water 

System Operations Models

Trinity River Basin

3406 (b)(23) Trinity River Restoration 

Program

San Joaquin River Basin

3406 (c)(1) San Joaquin River 

Restoration Program

Refuge Resources

3406 (b)(3) and 3406 (d)(2) Refuge 

Water Acquisition Program

3406 (d)(1), (d)(2), and (d)(5) 

Wheeling and Conveyance

3406 (d)(5) Facilities Construction 

and San Joaquin Basin Action Plan 

Lands

Other Resources

3404 Contract Renewals

3405 Water Transfers

3406 (b)(1) “other” Habitat 

Restoration Program

3408 (h) Land Retirement Program

CVP Water Operations Resources

3406 (b)(1)(B) Modified CVP 

Operations

3406 (b)(7) Flow Standards and 

Objectives

3406 (b)(8) Short Pulse Flows

3406 (b)(9) Flow Fluctuations

3406 (b)(19) Reservoir Storage

All Resource Areas

3406 (b)(5) Contra Costa Canal 

Pumping Plant

3406 (b)(6) Shasta Temperature 

Control Device 

3406 (b)(11) Coleman National Fish 

Hatchery

3406 (b)(17) ACID Diversion Dam 

3406 (b)(20) Glenn-Colusa Irrigation 

District Program

3406 (b)(22) Waterfowl Incentive 

Program

3406 (c)(2) Stanislaus River Basin 

Water Needs Program

3406 (d)(6) Central Valley Wetlands 

Supply

3406 (e) Supporting Investigations

3406 (f) Project Fisheries Impact 

Report

3408 (i) Water Conservation Program

3408 (j) Water Augmentation (Yield 

Study)
EXECUTIVE SUMMARY ES-

Rivers; environmental documents were developed 

for the Hammon Bar project on the Yuba River; and 

fish passage monitoring continued on the lower Yuba 

River. 

The Program also provided funding for a fish passage 

barrier assessment for Cow Creek and for the Mill 

Creek fish passage assessment and restoration 

project. 

San Joaquin Basin

The AFRP construction projects conducted in the 

San Joaquin basin in 2011 included the Budiselich 

Flashboard Dam boulder weir retrofit project on the 

Calaveras River; the placement of approximately 

28,000 cubic yards of material for floodplain and 

rearing habitat at the Merced River Ranch site; the 

placement of 6,557 tons of spawning gravel for the 

Mokelumne River Spawning Habitat Improvement

Project; spring pulse flows of 43,000 acre feet (AF) 

in the Mokelumne River to assist outmigrating juvenile 

salmon and steelhead through a joint settlement 

agreement with East Bay Municipal Utility District; 

the installation of VEMCO acoustic receivers in the 

San Joaquin River along with annual white sturgeon 

population assessments; the restoration of the 

Lancaster Road side channel in the Stanislaus River; 

and the Bobcat Flat Restoration Project to restore 

spawning, rearing and floodplain habitats in the 

Tuolumne River. 

The AFRP collected data and conducted reports on 

various riverine systems in the San Joaquin basin in 

2011. Studies were conducted in the Cosumnes, 

Merced, Lower Tuolumne, San Joaquin and Stanislaus 

Rivers on a variety of fish activities including fish 

collection and migration, flow management and 

technical project planning. 

The Program also provided funding to develop final 

designs, planning, and permitting to re-connect 

sloughs and floodplains within the Cosumnes River 

Preserve. The Service is a co-implementing agency at 

the Preserve.

Shasta Dam
ES-6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Dedicated 800,000 acre-feet (AF) Project 

Yield, 3406 (b)(2)

The full 800,000 AF of (b)(2) water was available 

for fish actions in water year 2011. And 348,800 AF 

was used. (b)(2) water was used on Clear Creek to 

augment base case flow and short pulse flows; on the 

Sacramento River to maintain 3,800 cfs flows; on the 

Stanislaus River to augment base case flows; and at 

CVP Jones Pumping Plant to reduce export flows.

Water Acquisition Program – Instream 

Water (Instream WAP), 3406 (b)(3) and (g)

The Instream WAP acquired 38,500 AF in the

Merced, Lower San Joaquin, and Stanislaus Rivers 

in support of the San Joaquin River Agreement and 

Vernalis Adaptive Management Plan.

Tracy (Jones) Pumping Plant, 3406 (b)(4)

The Program continued to fund actions at the Tracy 

Fish Collection Facility. At the Tracy Pumping Plant, 

engineering and biological assessments were 

conducted to improve the louver cleaner system and 

improve fish protection by reducing fish predation 

at the Tracy Fish Collection Facility. The Program 

also conducted studies to improve fish capture and 

reintroduction capabilities. 

Contra Costa Program (CCP), 3406 (b)(5)

The CCP finished the third and final construction 

phase of the 320-foot fish screen at Rock Slough. This 

was accomplished with funding from multiple sources, 

including American Recovery and Reinvestment Act 

(ARRA) funds. This project is discussed in more detail 

below in Recent Developments. 

Red Bluff Diversion Dam (RBDD), 3406 

(b)(10)

The RBDD Program permanently opened the Red 

Bluff Diversion Dam gates, lowering Lake Red Bluff 

to river channel levels and substantially improving 

the long-term availability of fish to pass upstream 

and downstream of the Red Bluff Diversion Dam. 

The Program continued sampling and studies on 

green sturgeon. Additionally, construction on the 

pumping plant and fish screen continued and is on 

schedule to deliver water to the Tehama Colusa 

Canal in FY 2012. This was accomplished with 

funding from multiple sources, including American 

Recovery and Reinvestment Act (ARRA) funds. This 

project is discussed in more detail below in Recent 

Developments.

Clear Creek Restoration Program (CCRP), 

3406 (b)(12)

On Clear Creek, more than 21,000 square feet of 

spawning habitat was created by gravel injections 

at five sites during 2011: below Whiskeytown Dam; 

below Dog Gulch Creek; above Peltier Bridge; at 

Paige Bar (below Peltier Bridge); and below NEED 

Camp (Guardian Rock site). Base flows of 200 cfs 

were provided between October 1 and May 31 

and pulse flows for spring-run Chinook were also 

provided. Water temperatures to maintain fish life 

cycles were partially met 77% of the time. Required 

instream dredging prevented the program from fully 

needing instream water temperature requirements. 

Two Instream Flow Methodology Reports (IFIMs) we

completed, bringing the total IFIMs complete for Clea

Creek to 14. 

Spawning and Rearing Habitat 

Restoration Program, 3406 (b)(13)

The Program created or improved spawning habitat 

by placing 5,000 tons of gravel in the Sacramento 

River; 5,000 tons in the Stanislaus River; and 20,770 

tons in the American River. Fish and water quality 

monitoring were also conducted to evaluate the 

effectiveness of the completed gravel injection 

projects.

Comprehensive Assessment and 

Monitoring Program (CAMP), 3406 (b)(16)

CAMP continued to support fisheries provisions 

through data acquisition, management and synthesis. 

Camp produced reports for the AFRP and produced a 

GIS-based tool to provide geospatial features related

to CVPIA projects. CAMP acquired new data to

quantify fish escapement on Cow and Cottonwood 

Creeks through video camera recordings. The 

program marked and tagged fish at hatcheries to 

estimate natural and hatchery production.

Anadromous Fish Screen Program 

(AFSP), 3406 (b)(21)

Construction on 4 fish screens was completed at the 

Sutter Mutual Portuguese Bend, Oji Brothers Farms, 

Windswept Land & Livestock; and the Patterson 

Fish Screen on the San Joaquin River. Construction 
EXECUTIVE SUMMARY ES-

continued on the American Basin (Natomas 

Mutual) Fish Screen Project (Sankey Diversion) 

with completion expected in FY 2013. Design, 

environmental compliance and permitting activities for 

the Yuba City and the Reclamation District 2035 Fish 

Screen projects continued in 2011 with construction 

commencement anticipated in FY 2012 and FY 2013, 

respectively. 

Ecosystem and Water Systems Operation 

Models , 3406 (g)

The models program modified the DSM2 model 

for low-lift pump operations at Old River temporary 

barriers; completed Version 1.0 of inSALMO, and 

extended the Sacramento River Water Quality Model 

from Knights Landing to Freeport; and continued 

development of the CalLite 2.0 water management 

model and user interface. CalLite 2.0 is expected to 

be available in FY 2012.

Trinity River Basin

The CVPIA includes provisions to authorize activities

for the Trinity River Restoration Program (TRRP); 

Section 3406 (b)(23) for delivering flows and 3406 

(b)(1) for river restoration. The goal of the TRRP is to 

restore and sustain natural production of anadromous 

fish populations downstream of Lewiston Dam to 

pre-dam levels, and to facilitate dependent Tribal, 

commercial, and sport fisheries’ full participation 

in the benefits of restoration via enhanced harvest 

opportunities. This will be accomplished through 

restoring habitats for the anadromous fishery 

resources by implementing variable annual instream 

flows, rehabilitating the channel, and managing 

sediment, as stipulated in the December 2000, 

Record of Decision (ROD), for the Trinity River 

Mainstem Fishery Restoration Final Environmental 

Impact Statement/Environmental Impact Report (E

EIR)

Trinity River Restoration Program, 

3406 (b)(1) “Other” and (b)(23) 2011 

Accomplishments 

The TRRP contributed to improving fisheries in FY 2011 

by managing flows, rehabilitating river channels and 

monitoring fish. The Program operated peak flows to 

allow an 11,600 cfs release to facilitate geomorphic 

processes within the channel. The Program completed 

Phase 2 of the Wheel Gulch channel rehabilitation 

project and added 5,300 cubic yards of course 

gravel to the river. Additionally, a significant 

funding obligation ($4 million) went towards stream 

assessments and fish monitoring for spawning habitat 

development.

San Joaquin River Basin

The CVPIA includes a provision to authorize activities

for the San Joaquin River Restoration Program (SJRRP) 

under Section 3406 (c)(1) of the Act. Implementation

activities, including planning and environmental 

studies are authorized also in the San Joaquin River 

Restoration Settlement (SJRRP) Act, included in the 

Omnibus Public Land Management Act of 2009. The 

SJRRP carries out activities to restore and maintain 

fish populations in “good condition” on the mainstem 

of the San Joaquin River while reducing or avoiding 

adverse water supply impacts to Friant Division longterm contractors. Specific actions to achieve these 

goals include reintroduction of spring-run Chinook 

salmon, restoration flow releases and recirculation of 

restoration flows back to Friant Division contractors. 

The SJRRP Act established the San Joaquin River 

Restoration Fund ($16.5 million obligated in FY 2011) 

and authorizes the use of up to $2 million a year from 

the Central Valley Project Restoration Fund under the 

Section 3406 (c)(1).

San Joaquin River Restoration Program, 

3406 (c)(1) 2011 Accomplishments

The San Joaquin River Restoration Program’s 

projects in 2011 included the Invasive Vegetation

Management and Control activities; the Annual 

Technical Report; and Annual Monitoring and 

Analysis Plan contributing toward the goals of 

reintroducing fish and maintaining fish populations in 

good condition.

CVP Water Operations Resource Area 

Goals

The CVPIA includes several programs in Section

3406 (b) that are designed to contribute to the 

biological resources by supplying optimal project 

water to resource locations in flow quantity, velocity 

and timing. Programs supporting this initiative include 

Section 3406 (b)(1)(B), Modified CVP Operations; 
ES-8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

and 3406 (b)(9)/(b)(19), Flow Fluctuations and 

Reservoir Storage. Two ongoing programs, Flow 

Standards and Objectives and Short Pulse Flows 

are incorporated into the operations of overarching 

programs such as Cleark Creek and Flow Fluctuations.

The Modified CVP Operations Program determines 

the instream flow needs in CVP streams by Instream

Flow Incremental Methodology (IFIM) studies th

focus solely on CVP streams: American, Sacramento, 

and Stanislaus rivers and Clear Creek. This habitatbased model was developed by the Service to assess 

instream flow needs for aquatic resources, including 

anadromous fish. The IFIM studies inform projec

managers how to vary CVP flows modifications 

depending on hydrology and biological conditions.

The Flow Fluctuations and Reservoir Storage Program 

seeks to maintain carryover water storage and deliver 

appropriately timed flows and flows of adequate 

quality to support fisheries restoration and meet other 

project purposes.

Modified CVP Operations, 3406 (b)(1)(B)

In FY 2011, the Program conducted Instream Flo

Incremental Methodology (IFIM) studies in Cle

Creek and the Stanislaus River. Both studies are 

expected to be completed in FY 2012. 

Results of completed studies were used to modify 

flows on both Clear Creek and the Sacramento River 

to improve conditions for fish habitat.

Flow Fluctuations and Reservoir Storage 

(FFP), 3406 (b)(9) and (19)

The FFP conducted salmon and steelhead surveys on 

the American River. The Program also collaborated 

with other members of the Stanislaus Operations 

Group to provide recommendations for achieving 

minimum instream flows and temperature objectives. 

Carryover targets at Shasta and Trinity Reservoirs 

were met in FY 2011.

Refuges Resources Area Goals

The CVPIA includes several provisions in Section

3406 (d) that are designed to contribute to the 

maintenance, restoration and enhancements of 

wetlands and waterfowl habitat. The Act directs 

Interior to: provide, either directly or through

contractual agreements with other appropriate 

parties, firm water supplies of suitable quality to 

maintain and improve wetland habitat areas on 19 

federal, state and private lands, collectively referred 

to as “refuges.” The Refuge Water Supply Program 

(RWSP) goal is to provide 555,515 AF of water 

annually, comprised of 422,251 AF of Level 2 water 

which also includes 26,007 AF of replacement water; 

and 133,264 AF of Incremental Level 4 water to the

refuges, as required by the Act. Full Level 4 water is 

the sum of Level 2 and Incremental Level 4 water

In addition and in response to findings and

recommendations of an independent scientific panel, 

a long-term strategy for achieving full Level 4 water 

supply reliability was drafted in 2011. The goal of 

this strategy is provide an approach, which includes 

completing construction of needed conveyance 

infrastructure and long-term measures for achieving 

full Level 4 reliability for all CVPIA designated refuges.

In 2012, it is planned to further refine this strategy

in cooperation with stakeholders including refuge 

agencies and managers and water users interest 

groups, and begin development of an implementation 

plan. 

2011 Accomplishments

Water Acquisitions Program – Refuge 

Water (Refuge WAP), 3406 (b)(3)(d)(2)

The Refuge WAP purchased 81,811 AF of water and 

acquired 22,511 AF through various other sources. 

The Program continued to fund Grasslands Water 

District’s Water Quality Monitoring Program in the 

Grasslands Ecological Area. The Program also 

completed construction of 2 wells at Volta Wildlife 

Area; construction was funded through the American 

Recovery and Reinvestment Act.

Refuge Water Conveyance, 3406 (d)(1),(2) 

and (5)

In FY 2011, the Refuge Water Conveyance Program

delivered 367,592 acre-feet of Level 2 water, 

including 26,007 AF of replacement water and 

101,854 acre-feet of Incremental Level 4 water. A

total of 55,343 AF of this water was from non-CVP 

diverse sources. For the first time, full allocation of 

Level 4 water was supplied to 11 of 14 South of Delta 

wildlife refuges with sufficient conveyance capabilities. 
EXECUTIVE SUMMARY ES-

Refuge Facilities Construction and 

San Joaquin Basin Action Plan Lands 

(SJBAPL), 3406 (d)(5)

The SJBAPL Program funded repairs to the East Bear 

Pumping Plant. Construction of the Gray Lodge/

Pixley Groundwater Well Project began in 2011 

consisting of 2 wells at Pixley NWR and 3 wells at 

Gray Lodge WA. These projects will provide for 

Level 2 water supplies.

Other Resources Area Goals

The fourth focus of the CVPIA restoration initiatives

is directed at terrestrial habitat and species; water 

quality and conservation; and contract renewals and 

transfers. Provisions supporting this initiative include 

Section 3406 (b)(1)“other,” Habitat Restoration 

Program (HRP); Section 3408 (h), Land Retirement 

Program (LRP); and Sections 3404 and 3405, 

Contract Renewals and Water Transfers. 

The HRP focuses on protecting native habitats 

that have been directly and indirectly affected 

by the CVP’s construction and operation. This is 

accomplished through the purchase of fee title or 

conservation easements on lands where threats 

are significant and restoring lands to native habitat, 

research, captive breeding and outreach activities. 

The HRP contributes to the protection and/or 

restoration of the 2.7 million acres of habitat affected 

by the construction and operation of the CVP. 

The LRP goals include the purchase and retirement 

of land from agricultural production to improve 

water quality and provide for terrestrial habitat 

restoration. By ceasing irrigation of agricultural lands, 

the LRP reduces the volume of agricultural drainage 

produced, improving water quality and providing the 

opportunity to restore wildlife habitat. Specifically, the 

goal of the LRP is to retire 15,000 acres of agricultural 

lands by 2014 for the Land Retirement Demonstration 

Project and to restore up to 400 acres of that land 

annually.

The Contract Renewals Program is authorized under 

the CVPIA, Section 3404 (c) to renew repayment and

water service contracts for the delivery of water from 

the CVP. In conjunction, the Water Transfers Program

under CVPIA, Section 3405, authorizes Interior t

approve the transfer of individual’s and district’s CVP 

water to other users within the state for any purpose 

recognized as beneficial under state law, subject to 

certain terms and conditions.

2011 Accomplishments

Habitat Restoration Program, 3406 (b)(1) 

“Other”

The HRP contributed to the protection of 5,404 acres 

of land through conservation easement acquisitions of 

2,407 acres of vernal pool, grassland, and riparian 

habitats at the Peek Ranch in Tehama County; and 

2,997 acres of vernal pool, grassland, and other 

habitats at the Kelsey Ranch in Merced. Additionally, 

the restoration of about 28 acres of alkali scrub 

and 101 acres of riparian woodland vegetation at 

the Panorama Vista Preserve in Kern County; and 

492 acres of serpentine grassland and associated 

habitats at Santa Teresa County Park in Santa 

Clara County occurred in 2011. The program also 

provided funds for research, captive breeding of 

critically endangered Lange’s metalmark butterfly, and 

outreach activities.

Land Retirement Program, 3408 (h)

The LRP restored approximately 260 acres of land 

from irrigated agricultural production at the Atwell 

Island Land Retirement Demonstration Project (LRDP)

site and converted it to native upland habitat (leaving 

750 acres left to reach the targeted goal of 15,000 

acres). Additionally, 39,463 AF of agricultural 

drainage water was reduced due to the removal of 

irrigation on LRDP lands.

Contract Renewals and Water Transfers, 

3404 (c) and 3405

To date, 88 long term renewal contracts and 27 

interim-renewal contracts have been executed within 

the various divisions of the CVP. There are 4 contracts 

that have completed negotiation for a long term 

contract, and 1 currently in long term negotiations. In

addition, 132 long term contracts have been renewed 

with the Sacramento River Water Right Settlement 

contractors and 1 is pending renewal upon expiration 

in July 2020. 

Reclamation approved the transfer of 898,123 

AF of CVP water in FY 2011. The majority of 

transfers stayed within current use from agricultural 
ES-10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Table ES-1: FY 2011 Funding Obligations by Program Activity (rounded)

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay Delta

Funds

ARRA

Funds Total Funds

3405(a) Water Transfer Program 0 0 0 166,420 0 166,420

3406(b)(1) Anadromous Fish Restoration Program 0 6,191,326 0 2,648,919 0 8,840,245

3406(b)(1) “other” – Habitat Restoration Program 0 1,698,730 0 4,151,986 0 5,850,716

3406(b)(1) “other” – Trinity River Restoration Program 8,655,938 988,819 0 0 41,296 9,686,053

3406(b)(2) Dedicated Project Yield 0 697,827 0 0 0 697,827

3406(b)(3) Water Acquisition Program 

-Instream Water (includes 

3408(g) [VAMP])

Instream water 0 711,230 0 0 0 711,230

VAMP 0 6,087,395 1,404,887 0 0 7,492,282

Level 4 250,000 12,616,343 0 0 0 12,866,343

3406(b)(4) Tracy (Jones) Pumping 

Plant Program

Tracy (Jones) 

Pumping Plant1

 2,173,487 (1,343) 0 0 0 2,172,144

Two Gates 0 0 0 13,162 0 13,162

3406(b)(5) Contra Costa Pumping Plant No. 1 13,396 0 0 4,622 2,435,970 2,453,988

3406(b)(9) Flow Fluctuations 0 35,691 0 0 0 35,691

3406(b)(10) Red Bluff Diversion Dam 22,267,909 0 2,704,647 0 7,289,444 32,262,000

3406(b)(12) Clear Creek Restoration Program 280,793 679,838 0 0 0 960,631

3406(b)(13) Spawning Gravel 0 899,951 0 0 0 899,951 

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 1,740,768 0 0 0 1,740,768

3406(b)(20) Glenn Colusa Irrigation District 36,288 0 0 0 0 36,288

3406(b)(21) Anadromous Fish Screen Program 349,200 3,877,085 0 2,000,000 0 6,226,285

3406(b)(23) Trinity River Restoration 3,503,949 0 0 127 0 3,504,076

3406(c)(1) San Joaquin River Comprehensive Plan 0 717,821 0 0 0 717,821

3406(d)(1) Refuge Water Supply Level 2 conveyance included in (d)(5)

3406(d)(2) Refuge Water Supply Level 4 acquisition included in (b)(3)

3406(d)(5) Refuge Facilities 

Construction Program

Construction 0 541,900 0 0 586,351 1,128,251

Wheeling 3,115,000 10,294,003 0 70,065 0 13,479,068

3406(d)(5) San Joaquin Basin Action Plan 95,294 16,680 0 0 0 111,974

3406(g) Models 0 603,607 0 0 0 603,607

3408(h) Land Retirement Program 62,456 483,660 0 0 0 546,116

3410 CVPIA Administration 726,203 0 0 0 0 726,203

TOTAL FUNDING OBLIGATED 41,529,913 48,881,331 4,109,534 9,055,301 10,353,061 113,929,140

1 A negative amount represents a recovery of a prior year obligation.
EXECUTIVE SUMMARY ES-1

Figure ES-2: FY 2011 Financial Obligations By Action Category

Figure ES-3: FY 2011 Financial Obligations By Fund Source
ES-12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

to agricultural and the second largest transfer 

classification was from agricultural to municipal and 

industrial use.

FUNDING 

Since FY 1993 Congress appropriated Restoration 

Fund and Water & Related Resources funds to the 

CVPIA Program. In addition, the program has bee

funded in part through other sources including State 

cost-share funds, Bay-Delta funds and the American 

Recovery and Reinvestment Act (ARRA) funding. From 

these combined sources, a total of $1.4 billion has 

been funded by CVPIA over the past 18 years.

FY 2011 

As shown in Table ES-1, a total of $113.9 million was 

obligated on CVPIA projects from a combination

of funding sources: Restoration Funds, Water and 

Related Resources, ARRA funds, Bay-Delta funds, 

and state cost share funds. Obligations by program 

activity and fund source are shown in Figures ES-2 

and ES-3.

State of California 

Cost-share 

Section 3406 of the CVPIA requires that the U.S. enter

into a cost-sharing agreement with the State for CVPIA

implementation. On June 27, 1994, the State and 

the U.S. entered into the Sharing of Costs Agreement 

for Mitigation Projects and Improvements (SCAMPI)

Initially under SCAMPI the State’s maximum amoun

payable was $50 million through the agreements 

expiration in December 31, 2008.

Amendment No. 1 to SCAMPI, executed in June

1998, specified that the maximum amount payable 

to the U.S. by the State under the CVPIA cost-share

was $93 million, the amount of funding provided by 

Proposition 204. Amendment No. 2 to SCAMPI,

executed in August 2001, increased the maximum 

amount payable by the State pursuant to the 

cost-share provisions of CVPIA to $162,110,000.

Amendment No. 3 to SCAMPI, executed in December

2008, resulted in an extension of SCAMPI for

an additional three years to December 31, 2011. 

Amendment No. 4 to SCAMPI, executed in February

2010, increased the maximum amount payable by the 

State pursuant to the cost-share provisions of CVPIA to

$167,610,000 for the Red Bluff Diversion Dam Task 

Order. Amendment No. 5 to SCAMPI, executed in

2011, increased the maximum amount payable to the 

U.S. by the State to $169,014,887 for the Vernalis 

Adaptive Management Plan (VAMP) Task Order 

Agreement. Amendment No. 6, also executed in 

2011, increased the maximum amount payable to the 

U.S. by the State to $175,514,887 towards the cost of 

the Fish Passage Improvement Project at the Red Bluff

Diversion Dam.

In 2011, the State, Reclamation and the Service

continued coordinating annual work plans in order 

to modify SCAMPI through Amendment No. 7 to

specify the maximum amount payable to the U.S. by 

the State for FY 2012 through FY 2014. Task Orders 

will document how the contributions will be made, 

either via cash or in-kind services, for various activities 

including Gravel Placement, Anadromous Fish 

Restoration Program, Models, Clear Creek Restoration 

Program, Comprehensive Assessment and Monitoring 

Program, and Refuges Program. These Task Orders 

and Amendment No. 7 are expected to be in place 

mid FY 2012. 

State Water Package

In 2010, the State legislature developed a measure

known as the Safe, Clean, and Reliable Drinking 

Water Supply Act. The purpose of the law is 

to protect water quality and ensure safe, clean 

drinking water; meet the water supply needs of 

California residents, farms, businesses; expand water 

conservation and recycling; restore fish and wildlife 

habitat; reduce polluted runoff that contaminates 

rivers, streams, beaches, and bays; and protect the 

safety of water supplies threatened by earthquakes 

and other natural disasters. The bond was originally 

slated to appear on the November 2, 2010, ballot 

as Proposition 18. However, on August 9, 2010, the 

California State Legislature decided to postpone the 

vote on the measure until the November 4, 2014, 

ballot.
EXECUTIVE SUMMARY ES-1

RECENT DEVELOPMENTS 

Independent Reviews for Refuges and 

Fisheries

Refuges

In 2008 and 2009, the Refuge Water Supply

Program was reviewed and the panel’s 

recommendations are presented in a report entitled, 

“Undelivered Water: Fulfilling the CVPIA Promise to

Central Valley Refuges”, dated November 3, 2009. 

The report found that even though the reliability of 

Level 2 water deliveries improved since 2002, Level 

4 water supplies had fallen short of CVPIA mandate

and prevented optimal performance of the Refuges. 

In response to the panel’s recommendations, the

Refuge WSP has taken several steps: entered into an 

agreement with the Service and the National Fish and 

Wildlife Foundation to explore avenues to improve 

the effectiveness of the water acquisitions, including 

those for Incremental Level 4; assessed ways to

increase the priority for pumping, conveyance and 

storage of Incremental Level 4 water supplies in CVP

facilities; continued planning for external conveyance 

construction; and investigated storage options in 

existing or new groundwater banks.

Fisheries

In 2007, as part of the Office of Management

and Budget (OMB) Program Assessment and 

Rating Tool (PART) process, the CVPIA Program

conducted two independent reviews to evaluate 

efficiency and effectiveness toward meeting the 

Act’s goals. A Fisheries Independent Review panel

assessed the implementation of the Central Valley 

fisheries activities (i.e. fish doubling). The panel’s 

recommendations can be found in, “Listen to the River 

– An Independent Report on the CVPIA Fisherie

Program” dated December 2008, which calls for 

a science-based adaptive management approach, 

increased focus on the Bay-Delta and increased 

flows for fish. Since the panel’s recommendations 

were released, the fifteen separate authorities that 

contribute to the “fish doubling” goal have been 

working together to implement improvements and 

to develop a fisheries resource area plan. This plan 

will articulate a reorganization strategy that places 

an emphasis on managing the fisheries related 

provisions as one program, rather than as individual 

program activities. This new structure will enable the 

program to articulate an overarching vision; utilize a 

science-based management framework to address 

problems at a system level; report accomplishments 

Salmon
ES-14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

by watershed; and improve transparency by 

communicating the coordination and decision-making 

that occurs within the program.

To address the panel’s recommendations, the 

Department of the Interior (DOI) is developing a

improved science-based decision making process 

update for fisheries. 

To coordinate CVPIA implementation to these

other fish protection and restoration efforts, 

DOI will develop an overarching strategy that

accommodates the species’ needs under the ESA 

and obligations under CVPIA using insights gained

through the Bay Delta Conservation Plan planning 

process, Interagency Ecological Program research

investigations, and other recovery efforts in the 

Central Valley. The revised strategy will facilitate 

future decisions using a scientific framework that 

connects restoration actions to environmental and 

population responses across watersheds. The 

recommendations in the Independent Review of the

CVPIA Fisheries Program and the Act’s goals will

guide the development of the revised strategy in light 

of the current regulatory and ecosystem conditions.

Specifically, the initial steps include developing the 

science-based decision process and producing an 

updated Implementation Plan. Key tasks include (1)

revising objectives for the CVPIA, (2) development of

system-wide model, (3) development of performance 

indices and monitoring efforts, and (4) scientific 

review. It is expected that the entire decision making

process with system-wide model, objectives and a 

recommendation for a supporting organizational 

structure will be complete by the end of FY 2013. 

This will enable FY 2014 project review to take full 

advantage of the new process. 

Operations Criteria And Plan (OCAP) 

And Biological Opinions In The Delta

On December 15, 2008, the Service issued its 

Biological Opinion (BiOp) analyzing the effects of 

the long-term coordinated operations of the CVP 

and SWP on the threatened delta smelt (2008 FWS 

OCAP BiOp). On June 4, 2009, NMFS issued 

its BiOp analyzing the effects of the coordinated 

operations of the CVP and SWP on threatened and 

endangered salmonids and other listed species 

(2009 NMFS OCAP BiOp). In each BiOp, the

consulting agency (Service or NMFS) concluded 

that the coordinated operations of the CVP and SWP 

are likely to jeopardize the continued existence of 

the listed species and to adversely modify critical 

habitat. Consequently, each BiOp included a 

reasonable and prudent alternative (RPA), developed 

by the fish agencies and intended to protect the listed 

species and habitat. Both BiOps were challenged 

in Federal District Court. On December 14, 2010, 

the District Court found the 2008 FWS OCAP BiOp 

to be arbitrary, capricious and unlawful, remanding 

the BiOp to the Service for further consideration. 

On September 20, 2011, the District Court similarly 

concluded that the 2009 NMFS OCAP BiOp was 

arbitrary, capricious, and unlawful, remanding it to 

NMFS for further consideration. The District Court did 

not vacate the two BiOps, so Reclamation and DWR 

continue to operate under them until the Service and 

NMFS issue new BiOps. 

In FY 2011, several key activities contributed to

meeting the RPA requirements. Examples include 

the implementation of a side-channel and floodplain 

restoration on the Stanislaus River by the Anadromous 

Fish Restoration Program. The Spawning and Rearing 

Habitat Restoration Program placed 5,000 tons of 

gravel in Goodwin Canyon on the Stanislaus River 

to increase and improve spawning habitat. And the 

Comprehensive Assessment and Monitoring Program 

used Rotary Screw Traps to monitor the production 

of juvenile Chinook salmon on the Stanislaus River, 

with the goal of assessing the effectiveness of habitat 

restoration in that watershed. 

Completion of Contra Costa

On September 19, 2011, Secretary of the Interior Ken

Salazar and Bureau of Reclamation Commissioner 

Michael Connor joined state, local and tribal officials 

to dedicate the Rock Slough Fish Screen project at 

the Contra Costa Canal Pumping Plant Number One. 

The fish screen, constructed through a partnership 

between Reclamation and the Contra Costa Water 

District, will help ensure a sustainable water supply, 

while protecting sensitive fish species and the 

ecosystem they inhabit. Completion of the project 

also helps fulfill requirements of the Central Valley 
EXECUTIVE SUMMARY ES-1

Project Improvement Act, Section 3406(b)(5), and the

2008 U.S. Fish and Wildlife Service’s Los Vaqueros 

Biological Opinion for the threatened Delta smelt. The 

fish screen project, which is substantially complete, is 

expected to be fully operational in November 2011.

Red Bluff Fish Passage

On September 1, 2011, Reclamation permanently 

opened the Red Bluff Diversion Dam gates, lowering 

Lake Red Bluff to river channel levels and substantially 

improving the long-term availability of fish to pass 

upstream and downstream of the Red Bluff Diversion 

Dam. The National Oceanic and Atmospheric 

Administration Fisheries Service’s Biological Opinion 

requires that the gates are opened no later than 

Sept. 1 to help migration of winter-run and spring-run 

Chinook salmon and green sturgeon past the dam site. 

Construction on the pumping plant and fish screens 

continues and the new plant is anticipated to come on 

line in FY2012.
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO
INTRODUCTIO 

Central Valley Project Improvemen

Chapter 1

Introduction
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

PURPOSE

This fiscal year (FY) 2011 CVPIA Annual

Accomplishments Report summarizes the actions 

authorized under the Central Valley Project 

Improvement Act (CVPIA or Act) of 1992 an

highlights FY 2011 accomplishments (October 1, 

2010 - September 30, 2011). Section 3408 (f) of 

the Act directs the Secretary of Interior to submit an

annual report describing all significant actions taken 

toward achievement of the intent and purposes of Title 

34. Accomplishments, funding obligations and recent 

developments for Section 3406 and 3408 CVPIA

Program activities are presented in Chapters 2, 3, 4, 

and 5 by resource area (Fisheries, Water Operations, 

Refuges, and Other Resources). The relevant Sections 

of the Act are provided for reference in Appendix B.

BACKGROUND

Central Valley Project Improvement 

Act of 1992

In 1992, the 102nd Congress passed, and the

President signed, the multi-purpose water legislation 

known as the CVPIA. Officially designated as Title

34 of Public Law 102-575, this landmark piece of 

legislation amends previous authorizations of the 

California Central Valley Project (CVP) to include fish 

and wildlife protection, restoration, enhancement, and 

mitigation as project purposes having equal priority 

with irrigations and domestic water supply uses, and 

power generation. 

The purpose of the CVPIA is expressed in six broad

statements found in Section 3402 of the Act: 

•	To protect, restore, and enhance fish, wildlife, 

and associated habitats in the Central Valley 

and Trinity River basins of California;

•	To address impacts of the CVP on fish, wildlife, 

and associated habitats; To improve the CVP’s 

operational flexibility;

•	To increase water-related benefits provided by 

the CVP to the state through expanded use of 

voluntary water transfers and improved water 

conservation;

•	To contribute to the state’s interim and longterm efforts to protect the San Francisco Bay/

Sacramento-San Joaquin Delta Estuary;

•	To achieve a reasonable balance among 

competing demands for use of CVP water, 

including the requirements of fish and wildlife, 

agricultural, municipal and industrial, and 

power contractors.

The Secretary of the Department of Interior (Interior

assigned primary responsibility for implementing 

CVPIA’s many provisions to Reclamation and the

Service, both agencies of Interior. Reclamation and

the Service coordinate with other federal agencies, 

tribes, the State of California (State), and numerous 

partners and stakeholders during each fiscal year to 

plan and implement activities. 

CVPIA Background

For 75 years, California has depended on the CVP 

for a large part of its water needs, particularly for 

agriculture. With a climate typified by extremely 

variable precipitation, both temporally and regionally, 

the State relies heavily on dams and reservoirs to 

balance and manage its water resources, and on 

an extensive distribution system to convey water 

supplies for regional needs. Much of the State’s water 

originates in the north and is conveyed southward, 

primarily through the Sacramento River system (see 

Figure 1). Some water is diverted along the way, 

with the remainder flowing into the Sacramento-San 

Joaquin River Delta, where CVP water co-mingles 

Chapter 1 - Introduction
INTRODUCTIO 

Figure 1: Central Valley Project (CVP) System
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

with other supplies such as those of the State Water 

Project (SWP). A portion of the water entering the 

delta is pumped south; the majority discharges to 

the San Francisco Bay and the Pacific Ocean. The 

CVP today comprises 18 dams and reservoirs (water 

storage capacity of 9 million acre-feet), 11 power 

plants, 500 miles of canals and aqueducts, three 

fish hatcheries, and associated facilities including 

pumping plants and power lines. The ecosystems of 

the Central Valley, Delta Estuary, San Francisco Bay, 

and Trinity River are affected by water diversions–

particularly in drought years–so much so that the 

courts have intervened to ensure that adequate 

fresh water enters these ecosystems. Compliance 

with the Endangered Species Act (ESA) and water 

quality mandates requires water releases from CVP 

dams to regulate water temperatures, salinity and 

instream flows, and limits water diversions to protect 

ESA-listed fish from the effects of pumping water at 

the Tracy (Jones) Pumping Plant in the Delta. These 

factors have greatly increased the competition for 

existing water supplies and have focused scrutiny 

on the ways that water resources are being used. 

Environmental conditions have changed greatly since 

the CVP was authorized in 1935. Population growth 

and development have increased farm, urban, and 

industrial water demands. Concurrently, populations 

of fish and wildlife have declined, resulting in some 

species being listed as endangered or threatened due 

to severe habitat loss. In response, a new imperative

for resource management and ecological stewardship 

has evolved. 

2011 Water Year

The Water Year type is a designation that is based 

on hydrologic indices for the Sacramento and San 

Joaquin Valleys. Water Year type is either wet, above 

normal, below normal, dry or critical. Water year 

type is determined by precipitation and is therefore 

indicative of local and regional conditions that 

influence climate, snowpack and runoff. Water Year 

2011 was classified as a wet year and when coupled 

with the above normal year in 2010, the abundance 

of water was a relief to the drought experienced from 

2007 through 2009. 

CVPIA Programs have seen varying effects from

the hydrology of 2010 and 2011. Biologically, the 

increased flows benefited aquatic species. For 

example, increases in outflow from the delta serve to 

trigger the migration of fish upstream. Preliminary, 

Chinook salmon returns through Central Valley 

streams appear to be on a positive, increasing trend 

since 2010.

However, the same water was a benefit to fish had 

minor negative effects to construction projects. Heavy 

rains encountered in November/December 2010 

and high flows in March 2011 flooded the work area 

and slowed construction at the Red Bluff Fish Passage 

Improvement Project

Overall and looking forward, this improved water 

condition is encouraging for the 2012 Water Year 

since the CVP will enter the next water year with 

improved reservoir carryover storage.

CVPIA GOALS

The current focus of the CVPIA Program is on fish

and wildlife restoration, water management, and 

conservation activities, authorized in Sections 

3406 and 3408 of the Act. These goals fit within 

three broad resource areas: Fisheries, Refuges and 

Other Resources. Figure 2 shows the active CVPIA

provisions that contribute to each resource area 

as well as those provisions that are completed or 

inactive. Additional information on the completed 

projects and how they have contributed to the CVPIA

restoration efforts may be found online at http://www.

usbr.gov/mp/cvpia/index.html. Contract renewals 

(Section 3404) and water transfers (Section 3405) 

goals are also important CVPIA goals and are

mentioned here, but are not the focus of this report 

since they are not funded with the CVPIA Restoration

Fund; their goals and accomplishments are briefly 

discussed in the Other Resources Chapter. 

A synopsis of the programs targets, status to date and 

2011 accomplishments are presented in Appendix A.

Two ongoing programs, Flow Standards and 

Objectives and Short Pulse Flows, are incorporated 

into the operations of overarching programs such as 

Cleark Creek and Flow Fluctuations.
INTRODUCTIO 

Fisheries Resource Area

Central Valley

The Act directs Interior to, “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 target established by 

this portion of the Act is known as the “fish-doubling 

goal”, which pertains to Chinook salmon, Rainbow 

trout (steelhead), striped bass, American shad, white 

sturgeon and green sturgeon; species believed 

to have been impacted by CVP construction and 

operation. Section 3406 (b)(1), which authorizes 

the Anadromous Fish Restoration Program (AFRP), is 

wholly devoted to the purpose of fish doubling. The 

AFRP’s 2001 Final Restoration Plan (Plan) identified 

289 actions and evaluations that were determined to 

be reasonable given numerous technical, legal and 

implementation considerations. The Plan’s actions and 

evaluations are covered in the October 1999 Central 

Valley Project Improvement Act Final Programmatic

Environmental Impact Statement. When the Plan’s

actions are implemented in concert, they provide for 

comprehensive restoration that improves freshwater 

habitat for Chinook salmon and other anadromous 

fish species.

In addition to the anadromous fish “doubling goal”,

the CVPIA Program uses the suite of structural and

non-structural restoration actions from the Plan to 

measure progress. Progress toward “fish doubling” 

Figure 2: Ongoing Programs by Resource Area and Completed Programs

Ongoing Programs Completed Programs

Fisheries Resources

Central Valley

3406 (b)(1) Anadromous Fish 

Restoration Program

3406(b)(2) Dedicated Project Yield

3406(b)(3) Instream Water Acquisition 

Program

3406 (b)(4) Tracy Pumping Plant 

Program

3406 (b)(10) Red Bluff Diversion Dam

3406 (b)(12) Clear Creek Restoration 

Program

3406 (b)(13) Spawning and Rearing 

Habitat Restoration Program

3406 (b)(15) Head of Old River 

Barrier

3406 (b)(16) Comprehensive 

Assessment and Monitoring Program

3406 (b)(21) Anadromous Fish 

Screen Program

3406 (g) Ecosystem and Water 

System Operations Models

Trinity River Basin

3406 (b)(23) Trinity River Restoration 

Program

San Joaquin River Basin

3406 (c)(1) San Joaquin River 

Restoration Program

Refuge Resources

3406 (b)(3) and 3406 (d)(2) Refuge 

Water Acquisition Program

3406 (d)(1), (d)(2), and (d)(5) 

Wheeling and Conveyance

3406 (d)(5) Facilities Construction 

and San Joaquin Basin Action Plan 

Lands

Other Resources

3404 Contract Renewals

3405 Water Transfers

3406 (b)(1) “other” Habitat 

Restoration Program

3408 (h) Land Retirement Program

CVP Water Operations Resources

3406 (b)(1)(B) Modified CVP 

Operations

3406 (b)(7) Flow Standards and 

Objectives

3406 (b)(8) Short Pulse Flows

3406 (b)(9) Flow Fluctuations

3406 (b)(19) Reservoir Storage

All Resource Areas

3406 (b)(5) Contra Costa Canal 

Pumping Plant

3406 (b)(6) Shasta Temperature 

Control Device 

3406 (b)(11) Coleman National Fish 

Hatchery

3406 (b)(17) ACID Diversion Dam 

3406 (b)(20) Glenn-Colusa Irrigation 

District Program

3406 (b)(22) Waterfowl Incentive 

Program

3406 (c)(2) Stanislaus River Basin 

Water Needs Program

3406 (d)(6) Central Valley Wetlands 

Supply

3406 (e) Supporting Investigations

3406 (f) Project Fisheries Impact 

Report

3408 (i) Water Conservation Program

3408 (j) Water Augmentation (Yield 

Study)
6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

goal and the restoration actions, as well as other 

CVPIA provisions that support the Central Valley

fisheries goals, and take part in implementing the 

Plan’s actions and evaluations are discussed in 

Chapter 2.

Trinity River Basin

The CVPIA includes provisions to authorize activities

for the Trinity River Restoration Program (TRRP); 

Section 3406 (b)(23) for delivering flows and 3406 

(b)(1) for river restoration. The Trinity River is the 

Klamath River’s largest tributary and is geographically 

separate from the Central Valley and the Sacramento 

River. However, substantial water from the Trinity 

River has historically been exported through a 

trans-basin diversion to support water needs in the 

Central Valley. The goal of the TRRP is to restore 

and sustain natural production of anadromous fish 

populations downstream of Lewiston Dam to pre-dam 

levels, to facilitate dependent tribal, commercial, 

and sport fisheries’ full participation in the benefits of 

restoration via enhanced harvest opportunities. This 

will be accomplished through restoring habitats for 

the anadromous fishery resources by implementing 

variable annual instream flows, rehabilitating the 

channel, and managing sediment. The TRRP carries 

out actions that are stipulated in the Record of 

Decision (ROD), signed on December 19, 2000, 

the Trinity River Mainstem Fishery Restoration Final 

Environmental Impact Statement/Environmental

Impact Report (EIS/EIR), completed in October 20

San Joaquin River Basin

The San Joaquin River Restoration Program (SJRRP) 

carries out activities to restore and maintain fish 

populations in “good condition” on the mainstem of 

the San Joaquin River while reducing or avoiding 

adverse water supply impacts to Friant Division longterm contractors. Specific actions to achieve these 

goals include reintroduction of spring-run Chinook 

salmon, restoration flow releases and recirculation of 

restoration flows back to Friant Division contractors. 

The SJRRP is being planned and implemented 

because of the Natural Resources Defense Council, 

et al., v. Kirk Rodgers, et al. Stipulation of SJRRP 

Settlement (Settlement). Implementation of the

Settlement, including planning, environmental 

studies and other activities necessary to achieve the 

Settlement’s Restoration and Water Management 

goals are authorized in the San Joaquin River 

Restoration Settlement (SJRRP) Act, included in the 

Omnibus Public Land Management Act of 2009. The 

Act, which authorizes and directs the Secretary to fully 

implement the Settlement, was signed by the President 

on March 30, 2009, and became Public Law 111-11. 

The Act established the San Joaquin River Restoration 

Fund (SJRR Fund) and authorizes the use of up to 

$2 million a year from the Central Valley Project 

Restoration Fund under the Section 3406 (c)(1).

While the fisheries sections are currently administered 

individually, the Science Based Management 

Framework approach discussed below under Recent 

Developments aims to coordinate, integrate and 

prioritize CVPIA efforts across geographic areas.

CVP Water Operations Resource Area 

Goals

The CVPIA includes several provisions in Section

3406 (b) that are designed to contribute to the 

biological resources by supplying optimal project 

water to resource locations in flow quantity, velocity 

and timing. Provisions supporting this initiative include 

Section 3406 (b)(1)(B), Modified CVP Operations; 

and 3406 (b)(9)/(b)(19), Flow Fluctuations and 

Reservoir Storage.

Refuges Resources Area

The CVPIA includes several provisions in Section

3406 (d) that are designed to contribute to the 

maintenance, restoration and enhancements of 

wetlands and waterfowl habitat. The Act directs 

Interior to: provide, either directly or through

contractual agreements with other appropriate 

parties, firm water supplies of suitable quality to 

maintain and improve wetland habitat areas on 19 

federal, state and private lands, collectively referred 

to as “refuges.” The Refuge Water Supply Program 

(RWSP) goal is to provide 555,515 AF of water 

annually, including 422,251 AF of Level 2 water; 

26,007 AF of replacement water; and 133,264 AF of 

Incremental Level 4 water to the refuges, as required

by the Act. 

Based upon a wet year hydrology, Reclamation 

committed in 2011 to provide full Level 4 water (Level 

2 plus Incremental Level 4) to South-of-Delta refuges

capable of receiving such water. This is the first year 
INTRODUCTIO 

this has been achieved since enactment of CVPIA in

1992. 

Other Resources Area

The third focus of the CVPIA restoration initiatives is

directed at terrestrial habitat and species; and water 

quality and conservation. Provisions supporting 

this initiative include the Section 3406 (b)(1)“other” 

Habitat Restoration Program (HRP), which focuses 

on protecting native habitats that have been directly 

and indirectly affected by the CVP’s construction and 

operation. This is accomplished through the purchase 

of fee title or conservation easements on lands where 

threats are significant and restoring lands to native 

habitat, research, captive breeding and outreach 

activities. The HRP contributes to the protection and/

or restoration of the 2.7 million acres of habitat 

affected by the construction and operation of the CVP. 

The Land Retirement Program (LRP), Section 3408 

(h), goals include the purchase and retirement of 

land from agricultural production to improve water 

quality and provide for terrestrial habitat restoration. 

By ceasing irrigation of agricultural lands, the 

LRP reduces the volume of agricultural drainage 

produced, improving water quality and providing the 

opportunity to restore wildlife habitat. Specifically, the 

goal of the LRP is to retire 15,000 acres of agricultural 

lands by 2014 for the Land Retirement Demonstration 

Project and to restore up to 400 acres of that land 

annually.

FUNDING

CVPIA fish, wildlife, and improved water management

and conservation actions are implemented through 

a variety of agreements that are held with partners 

including other federal and State agencies, tribes 

and local organizations. Reclamation and the 

Service use interagency agreements, memoranda of 

understanding, grants and cooperative agreements to 

partner with entities that have the authority, interest, 

ability, expertise and/or resources to implement 

CVPIA restoration actions

The CVPIA Program utilizes multiple funding sources:

CVP Restoration Fund (RF), Water and Related 

Resources (W&RR), Bay-Delta Fund, American 

Recovery and Reinvestment Act Fund (ARRA), and the 

State of California (State). The Act specifies funding 

for each provision should either be reimbursable, 

non-reimbursable, from the State; or a combination of 

these sources. The RF, established by Section 3407(d) 

of the CVPIA, is an account in the Treasury of the

United States (U.S.) and consists largely of revenue 

generated by fees levied on CVP water and power 

users. The total maximum annual RF appropriation 

authorized by CVPIA is $50 million (1992 price

levels). Of this, $30 million (1992 price level) is the 

maximum amount (payment ceiling) that is authorized 

to be assessed and collected from the water and 

power users. The $30 million payment ceiling is 

calculated on a 3-year rolling average, which results 

in a cyclical funding pattern when collections are 

limited by the water deliveries and appropriations 

are limited by Congress. The annual appropriation 

bill from Congress provides budget authority based 

on estimated collections, and the obligation of these 

funds can only occur after the collections are made. 

Funding Obligations to Date

Since FY 1993, Congress appropriated RF and W&RR 

funds to the CVPIA Program. In addition, funds hav

Friant Dam
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Figure 3: Program Financial Obligations By Action Category to Date

Figure 4: Program Financial Obligations By Fund Source to Date
INTRODUCTIO 

been obligated from State cost-share funds, Bay-Delta 

funds and the American Recovery and Reinvestment 

Act (ARRA) funding. From these combined sources, a 

total of $1.4 billion has been obligated by the CVPIA

Program over the past 18 years, as shown in Figures 3 

and 4. 

Total obligations to date include funding for the 

CVPIA program management and administration

function. As shown in Figure 3, since FY 1993 a total 

of $13.3 million has been obligated for this critical 

oversight function. The CVPIA administration program

provides financial management and reporting, longterm planning and establishes program priorities, and 

coordinates development of annual work plans. 

Revisions to FY 2010 Report

Program Administration funding was omitted from the 

FY 2010 report, but has been included in this report. 

Funding obligations to date have also been revised to 

report an additional $6.5 million that was obligated 

in FY 2010 from ARRA funds to construct groundwater 

wells at the Gray Lodge and Volta Wildlife Areas, 

and an additional $1.8 million obligated in FY 2010 

for land acquisition related to the Fish Passage 

Improvement Program at the Red Bluff Diversion Dam.

FY 2011 

For FY 2011, $49.9 million was appropriated to the 

Restoration Fund. Total payments to the Restoration 

fund were $51.2 million. The difference between 

appropriations and payments in the amount of 

$1.3 million remains in a treasury account until 

appropriated for use. 

As shown in Figures 5 and 6, a total of $113.9 million 

was obligated on CVPIA projects from a combination

of funding sources: Restoration Funds ($48.9 million), 

Water and Related Resources ($41.5 million), ARRA 

funds ($10.4 million), state cost share funds ($4.1 

million), and Bay-Delta funds ($9.0 million). See 

Table 1 for a breakdown of funding for each CVPIA

Program activity in FY 2011.

American Recovery and Reinvestment 

Act (Arra) Funding

ARRA’s funding in FY 2011 enhanced the CVPIA

Program’s capabilities to restore fisheries and wildlife 

refuges. To date, approximately $151 million has 

been awarded to Reclamation for CVPIA Program

activities. In FY 2011, ARRA funds were obligated

for the following: Contra Costa Canal Pumping Plant 

Program, 3406 (b)(5), obligated $2.4 million to 

complete construction on the Contra Costa Canal fish 

screen; Red Bluff Diversion Dam Program, 3406 (b)

(10), obligated $7.3 million to continue construction 

on the permanent pumping plant for the fish passage 

project, which is scheduled to be complete in FY 

2012; and the RWSP obligated $0.6 million to 

complete construction of groundwater wells at the 

Pixley National Wildlife Refuge, the Gray Lodge 

State Wildlife Area, and the Volta State Wildlife Area. 

ARRA funding for future years will continue to be 

reduced over previous years. 

State of California 

Cost-share 

Section 3406 of the CVPIA requires that the U.S.

enter into a cost-sharing agreement with the State 

for CVPIA implementation. On June 27, 1994, the

State and the U.S. entered into the Sharing of Costs 

Agreement for Mitigation Projects and Improvements

(SCAMPI). Initially under SCAMPI the State

maximum amount payable was $50 million through 

the agreements expiration in December 31, 2008.

Amendment No. 1 to SCAMPI, executed in June

1998, specified that the maximum amount payable 

to the U.S. by the State under the CVPIA cost-share

was $93 million, the amount of funding provided by 

Proposition 204. Amendment No. 2 to SCAMPI,

executed in August 2001, increased the maximum 

amount payable by the State pursuant to the 

cost-share provisions of CVPIA to $162,110,000.

Amendment No. 3 to SCAMPI, executed in December

2008, resulted in an extension of SCAMPI for

an additional three years to December 31, 2011. 

Amendment No. 4 to SCAMPI, executed in February

2010, increased the maximum amount payable by the 

State pursuant to the cost-share provisions of CVPIA to

$167,610,000 for the Red Bluff Diversion Dam Task 

Order. Amendment No. 5 to SCAMPI, executed in

2011, increased the maximum amount payable to the 

U.S. by the State to $169,014,887 for the Vernalis 

Adaptive Management Plan (VAMP) Task Order 

Agreement. Amendment No. 6, also executed in 

2011, increased the maximum amount payable to the 
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Figure 5: FY 2011 Financial Obligations By Action Category

Figure 6: FY 2011 Financial Obligations By Fund Source
INTRODUCTIO  

Table 1: FY 2011 Funding Obligations by Program Activity (rounded)

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay Delta

Funds

ARRA

Funds Total Funds

3405(a) Water Transfer Program 0 0 0 166,420 0 166,420

3406(b)(1) Anadromous Fish Restoration Program 0 6,191,326 0 2,648,919 0 8,840,245

3406(b)(1) “other” – Habitat Restoration Program 0 1,698,730 0 4,151,986 0 5,850,716

3406(b)(1) “other” – Trinity River Restoration Program 8,655,938 988,819 0 0 41,296 9,686,053

3406(b)(2) Dedicated Project Yield 0 697,827 0 0 0 697,827

3406(b)(3) Water Acquisition Program 

-Instream Water (includes 

3408(g) [VAMP])

Instream water 0 711,230 0 0 0 711,230

VAMP 0 6,087,395 1,404,887 0 0 7,492,282

Level 4 250,000 12,616,343 0 0 0 12,866,343

3406(b)(4) Tracy (Jones) Pumping 

Plant Program

Tracy (Jones) 

Pumping Plant1

 2,173,487 (1,343) 0 0 0 2,172,144

Two Gates 0 0 0 13,162 0 13,162

3406(b)(5) Contra Costa Pumping Plant No. 1 13,396 0 0 4,622 2,435,970 2,453,988

3406(b)(9) Flow Fluctuations 0 35,691 0 0 0 35,691

3406(b)(10) Red Bluff Diversion Dam 22,267,909 0 2,704,647 0 7,289,444 32,262,000

3406(b)(12) Clear Creek Restoration Program 280,793 679,838 0 0 0 960,631

3406(b)(13) Spawning Gravel 0 899,951 0 0 0 899,951 

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 1,740,768 0 0 0 1,740,768

3406(b)(20) Glenn Colusa Irrigation District 36,288 0 0 0 0 36,288

3406(b)(21) Anadromous Fish Screen Program 349,200 3,877,085 0 2,000,000 0 6,226,285

3406(b)(23) Trinity River Restoration 3,503,949 0 0 127 0 3,504,076

3406(c)(1) San Joaquin River Comprehensive Plan 0 717,821 0 0 0 717,821

3406(d)(1) Refuge Water Supply Level 2 conveyance included in (d)(5)

3406(d)(2) Refuge Water Supply Level 4 acquisition included in (b)(3)

3406(d)(5) Refuge Facilities 

Construction Program

Construction 0 541,900 0 0 586,351 1,128,251

Wheeling 3,115,000 10,294,003 0 70,065 0 13,479,068

3406(d)(5) San Joaquin Basin Action Plan 95,294 16,680 0 0 0 111,974

3406(g) Models 0 603,607 0 0 0 603,607

3408(h) Land Retirement Program 62,456 483,660 0 0 0 546,116

3410 CVPIA Administration 726,203 0 0 0 0 726,203

TOTAL FUNDING OBLIGATED 41,529,913 48,881,331 4,109,534 9,055,301 10,353,061 113,929,140

1 A negative amount represents a recovery of a prior year obligation.
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

U.S. by the State to $175,514,887 towards the cost of 

the Fish Passage Improvement Project at the Red Bluff

Diversion Dam.

In 2011, the State, Reclamation and the Service

continued coordinating annual work plans in order 

to modify SCAMPI through Amendment No. 7 to

specify the maximum amount payable to the U.S. 

by the State for FY 2012 through FY 2014. Task 

Orders will document how the contributions will be 

made, either via cash or in-kind services, for various 

activities including Gravel Placement, Anadromous 

Fish Restoration Program, Models, Clear Creek 

Restoration Program, Comprehensive Assessment and 

Monitoring Program, and Refuges Program. These 

Task Orders and Amendment No. 7 are expected to 

be in place mid FY 2012. 

State Water Package

In FY 2010, the State legislature developed a

measure known as the Safe, Clean, and Reliable 

Drinking Water Supply Act. The purpose of the law 

is to protect water quality and ensure safe, clean 

drinking water; meet the water supply needs of 

California residents, farms, businesses; expand water 

conservation and recycling; restore fish and wildlife 

habitat; reduce polluted runoff that contaminates 

rivers, streams, beaches, and bays; and protect the 

safety of water supplies threatened by earthquakes 

and other natural disasters. It includes State issuance

of bonds totaling $11.140 billion paid from existing 

State funds. The measure contains funding for CVPIA

Program activities such as Central Valley wildlife 

refuge water and construction of fish passage 

improvements at Red Bluff Diversion Dam. The bond 

was originally slated to appear on the November 

2, 2010, ballot as Proposition 18. However, on 

August 9, 2010, the California State Legislature 

decided to postpone the vote on the measure until the 

November 4, 2014, ballot. 

As a result of the State Water Package, the 

State appropriated $28 million in funding from 

Proposition 50, to fund the Two-Gates Fish Protection 

Demonstration Program. However, the independent 

review of the Two Gates Demonstration Project found 

additional data is needed to assess its effectiveness in 

achieving its objectives. Once the data are obtained 

and assessed, a determination on whether the project 

should move forward will be made. Reclamation 

is working with DWR and the State Water Project 

contractors to develop additional actions that could 

be implemented in addition to and/or as alternatives 

to the Two-Gates Project.

RECENT DEVELOPMENTS 

Since 1993, the CVPIA Program has steadily

progressed in completing specific actions called 

for by Congress to meet the goals of CVPIA. The

Program has also grown in complexity in response 

to key changes that have affected the operation 

of Central Valley Project (CVP), vulnerable status 

of key anadromous fish species, development of a 

better understanding of species life cycle needs, 

and the emergence of new scientific tools. Several 

developments in FY 2011 affected the planning and 

implementation including progress on the Science 

Based Management Framework, OCAP and the 

Biological Opinions in the Bay-Delta, State cost-share 

funding, the State Water Package, the Bay Delta 

Conservation Plan, and changing environmental 

factors. Also, as a result of continued program 

implementation, the Contra Costa Canal Pumping 

Plant project was completed in 2011 as was the 

permanent operational change of the Red Bluff 

Diversion Dam gates. 

Independent Reviews for Refuges and 

Fisheries

Refuges

In 2008 and 2009, the Refuge Water Supply

Program (Refuge WSP) was reviewed and the panel’s 

recommendations are presented in a report entitled, 

“Undelivered Water: Fulfilling the CVPIA Promise to

Central Valley Refuges”, dated November 3, 2009. 

The report found that even though the reliability of 

Level 2 water deliveries improved since 2002, Level 

4 water supplies had fallen short of CVPIA mandate

and prevented optimal performance of the Refuges. 

In response to the panel’s recommendations, the

Refuge WSP has taken several steps: entered into an 

agreement with the Service and the National Fish and 

Wildlife Foundation to explore avenues to improve 

the effectiveness of the water acquisitions, including 

those for Incremental Level 4; assessed ways to
INTRODUCTIO  

increase the priority for pumping, conveyance and 

storage of Incremental Level 4 water supplies in CVP

facilities; continued planning for external conveyance 

construction; and investigated storage options in 

existing or new groundwater banks.

Fisheries

In 2007, as part of the Office of Management

and Budget (OMB) Program Assessment and 

Rating Tool (PART) process, the CVPIA Program

conducted two independent reviews to evaluate 

efficiency and effectiveness toward meeting the 

Act’s goals. A Fisheries Independent Review panel

assessed the implementation of the Central Valley 

fisheries activities (i.e. fish doubling). The panel’s 

recommendations can be found in, “Listen to the River 

– An Independent Report on the CVPIA Fisherie

Program” dated December 2008, which calls for 

a science-based adaptive management approach, 

increased focus on the Bay-Delta and increased 

flows for fish. Since the panel’s recommendations 

were released, the fifteen separate authorities that 

contribute to the “fish doubling” goal have been 

working together to implement improvements and 

to develop a fisheries resource area plan. This plan 

will articulate a reorganization strategy that places 

an emphasis on managing the fisheries related 

provisions as one program, rather than as individual 

program activities. This new structure will enable the 

program to articulate an overarching vision; utilize a 

science-based management framework to address 

problems at a system level; report accomplishments 

by watershed; and improve transparency by 

communicating the coordination and decision-making 

that occurs within the program.

To address the panels recommendations, the 

Department of the Interior (DOI) is developing a

improved science-based decision making process 

update for fisheries.

To coordinate CVPIA implementation to these

other fish protection and restoration efforts, 

DOI will develop an overarching strategy that

accommodates the species’ needs under the ESA 

and obligations under CVPIA using insights gained

through the Bay Delta Conservation Plan planning 

process, Interagency Ecological Program research

Bridge and Siphon under Red Bank Creek complete in FY-2011. Looking from Sacramento River upstream along Red Bank 

Creek.
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

investigations, and other recovery efforts in the 

Central Valley. The revised strategy will facilitate 

future decisions using a scientific framework that 

connects restoration actions to environmental and 

population responses across watersheds. The 

recommendations in the Independent Review of the

CVPIA Fisheries Program and the Act’s goals will

guide the development of the revised strategy in light 

of the current regulatory and ecosystem conditions. 

Specifically, the initial steps include developing the 

science-based decision process and producing an 

updated Implementation Plan. Key tasks include (1)

revising objectives for the CVPIA, (2) development of

system-wide model, (3) development of performance 

indices and monitoring efforts, and (4) scientific 

review. It is expected that the entire decision making

process with system-wide model, objectives and a 

recommendation for a supporting organizational 

structure will be complete by the end of FY 2013. 

This will enable FY 2014 project review to take full 

advantage of the new process. 

Operations Criteria and Plan (OCAP) 

and Biological Opinions In the Delta

On December 15, 2008, the Service issued its 

Biological Opinion (BiOp) analyzing the effects of 

the long-term coordinated operations of the CVP 

and SWP on the threatened delta smelt (2008 FWS 

OCAP BiOp). On June 4, 2009, NMFS issued 

its BiOp analyzing the effects of the coordinated 

operations of the CVP and SWP on threatened and 

endangered salmonids and other listed species 

(2009 NMFS OCAP BiOp). In each BiOp, the

consulting agency (Service or NMFS) concluded 

that the coordinated operations of the CVP and SWP 

are likely to jeopardize the continued existence of 

the listed species and to adversely modify critical 

habitat. Consequently, each BiOp included a 

reasonable and prudent alternative (RPA), developed 

by the fish agencies and intended to protect the listed 

species and habitat. Both BiOps were challenged 

in Federal District Court. On December 14, 2010, 

the District Court found the 2008 FWS OCAP BiOp 

to be arbitrary, capricious and unlawful, remanding 

A local population of Tipton kangaroo rats has benefitted from Land Retirement at the Atwell Island Site. The Tipton kangaroo rat 

is a federal and state listed species.
INTRODUCTIO  

the BiOp to the Service for further consideration. 

On September 20, 2011, the District Court similarly 

concluded that the 2009 NMFS OCAP BiOp was 

arbitrary, capricious, and unlawful, remanding it to 

NMFS for further consideration. The District Court did 

not vacate the two BiOps, so Reclamation and DWR 

continue to operate under them until the Service and 

NMFS issue new BiOps. 

In FY 2011, several key activities contributed to

meeting the RPA requirements. Examples include 

the implementation of a side-channel and floodplain 

restoration on the Stanislaus River by the Anadromous 

Fish Restoration Program. The Spawning and Rearing 

Habitat Restoration Program placed 5,000 tons of 

gravel in Goodwin Canyon on the Stanislaus River 

to increase and improve spawning habitat. And the 

Comprehensive Assessment and Monitoring Program 

used Rotary Screw Traps to monitor the production 

of juvenile Chinook salmon on the Stanislaus River, 

with the goal of assessing the effectiveness of habitat 

restoration in that watershed. 

In FY 2011, a key activity that contributed to meeting

the RPA requirements was the implementation of sidechannel and floodplain restoration on the Stanislaus 

River. This project strives to restore freshwater 

migratory habitat for juvenile steelhead by increasing 

floodplain connectivity and reducing predation risk 

during migration (Section 3406 (b) (1)). 

Completion of Contra Costa

On September 19, 2011, Secretary of the Interior Ken

Salazar and Bureau of Reclamation Commissioner 

Michael Connor joined state, local and tribal 

officials to dedicate the Rock Slough Fish Screen 

project at the Contra Costa Canal Pumping Plant 

Number One. The fish screen, constructed through 

a partnership between Reclamation and the Contra 

Costa Water District, will help ensure a sustainable 

water supply and a strong economy for California, 

while protecting sensitive fish species and the 

ecosystem they inhabit. Completion of the project 

also helps fulfill requirements of the Central Valley 

Project Improvement Act, Section 3406(b)(5), and the

2008 U.S. Fish and Wildlife Service’s Los Vaqueros 

Biological Opinion for the threatened Delta smelt.

The Rock Slough project, which was awarded $25.6 

million in ARRA funds, completes the screening of 

the last of CCWD’s four Delta intakes for protection 

of resident and migratory fish species, including the 

threatened Delta smelt and other threatened and 

endangered fish species that might otherwise be 

drawn in from the Delta.

The fish screen project, which is substantially 

complete, is expected to be fully operational in 

November 2011.

Red Bluff Fish Passage

The overall goal of CVPIA Section 3406 (b)(10),

Red Bluff Fish Passage, is to substantially improve the 

long-term availability of fish to pass upstream and 

downstream of the Red Bluff Diversion Dam. A major 

milestone was accomplished towards this end when 

on September 1, 2011, Reclamation permanently 

opened the Diversion Dam gates and lowered Lake 

Red Bluff to river channel levels. Thus, Reclamation 

is now able to comply with the National Oceanic 

and Atmospheric Administration Fisheries Service’s 

Biological Opinion that requires the gates are opened 

no later than Sept. 1 to help migration of winter-run 

and spring-run Chinook salmon and green sturgeon 

past the dam site. 

Construction on the pumping plant and fish screens 

continues and the new plant is anticipated to come on 

line in FY2012.

Central Valley Project Improvemen

Chapter 2

FISHERIES

RESOURCE 

AREA
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

The Anadromous Fish Restoration Program (AFRP) is 

the overarching program to address anadromous fish 

doubling in the Central Valley. Natural production 

of anadromous fish is an outcome based goal of the 

CVPIA Program. The Act specifically directs Interior t

“... 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...”

Central Valley rivers and streams were defined in 

the January 9, 2001, Final Restoration Plan for the 

AFRP as all rivers, streams, creeks, sloughs and other 

watercourses, regardless of volume and frequency 

of flow, that drain into the Sacramento River basin, 

the San Joaquin River basin downstream of Mendota 

Pool, or the Sacramento-San Joaquin Delta upstream 

of Chipps Island and the 22 main rivers and streams

are specifically called out within Appendix B of that 

document.

The anadromous fish production targets pertain to 

Chinook salmon, steelhead, striped bass, American 

shad, white sturgeon, and green sturgeon, which are 

believed to have been affected by CVP construction 

and operation.

Subsequent to CVPIA’s passage, the AFRP developed

a series of planning reports that culminated in the Final 

AFRP Restoration Plan (Final Restoration Plan) (FRP) 

in 2001. As acknowledged in the CVPIA Record of

Decision (ROD), the Final Restoration Plan guides the 

implementation of the actions and evaluations which 

were developed to address the doubling goal. The 

289 actions and evaluations in the Final Restoration 

Plan are categorized by six programmatic-level 

objectives:

•	Improve habitat for all life stages of anadromous

fish through provision of flows of suitable quality, 

quantity, and timing, and improved physical 

habitat 

•	Improve survival rates by reducing or

eliminating entrainment of juveniles at diversions 

•	Improve the opportunity for adult fish to reach

their spawning habitats in a timely manner 

•	Collect fish population, health, and habitat data 

to facilitate evaluation of restoration actions

•	Integrate habitat restoration efforts with harvest

and hatchery management 

•	Involve partners in implementing and evaluating

restoration actions

The actions and evaluations identified in the Final 

Restoration Plan are annotated within the following 

text by number.

PERFORMANCE MEASURES

The AFRP goal is to at least double the natural 

production of anadromous fish from the baseline 

average established during 1967–1991, and to 

maintain that population on a long-term, sustainable 

basis. Table 2 below lists the doubling target by 

species. The AFRP implements actions that will 

contribute to the doubling of the natural production of 

anadromous fish populations. To achieve the fishdoubling goal, the AFRP has identified 289 actions 

and evaluations that support Fisheries restoration 

(Table 3). The CVPIA Program Activity Review Report

identified 128 Restoration Plan high and medium 

Anadromous Fish Restoration 

Program

3406 (b)(1)
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

Table 2: Yearly Estimates of Natural Production of Anadromous Fish and the Average Natural

 Production by Species within Central Valley River and Streams, 1992-2010

Chinook Salmon Run

Year Steelheada

American 

Shadb

Striped 

Bassc

Green 

Sturgeond

White 

Sturgeone Fall Late Fall Winter Spring

Baseline 6,546 2,129 1,252,259 983 5,571 374,049 34,192 54,439 34,374

Doubling

Target

13,000 4,300 2,500,000 2,000 11,000 750,000 68,000 110,000 68,000

1992 4,086 2,010 777,293 193,447 27,576 3,144 4,440

1993 5,153 656,506 68 692 320,533 2,369 1,024 4,157

1994 1,318 599,770 6,392 385,842 1,047 505 7,720

1995 6,803 714,930 764 4,182 36,474

1996 4,260 1,043,239 490,236 447 2,112 6,213

1997 2,591 1,306 11,689 604,049 1,344 2,010 3,866

1998 4,134 1,356,412 470 8,971 278,730 82,190 5,613 49,172

1999 715 403,023 17,243 5,439 11,130

2000 764 1,591,419 661,554 19,894 2,657 11,583

2001 761 7,098 5,129 530,504 27,717 9,916 18,401

2002 1,914 945,878 1,688 2,775 542,633 56,662 9,195 19,839

2003 9,342 829,111 528,336 9,106 10,882 13,269

2004 947 1,312,452 512,629 21,244 14,763 21,530

2005 1,741 1,017,116 2,557 2,898 397,755 20,838 21,511 26,099

2006 2,303 3,144 6,991 227,985 15,600 19,712 11,659

2007 551 1,019,511 1,530 10,559 107,253 30,509 4,142 13,138

2008 271 938,965 1,330 6,257 39,778 4,806 2,555 4,489

2009 624 922,622 10,272 6,258 30,604 4,350 4,070 2,492

2010 683 684,486 102,821 5,577 1,552 2,064

Average

% of 

Goal

N/A

N/A

2,468

57%

 978,199

39%

2,948

147%

6,237

57%

372,344

50%

18,383

27%

 6,578

6%

 14,091

21%

 

a Insufficient data are available to estimate natural production of steelhead in the Central Valley other than upstream of Red Bluff Diversion Dam. 

Operational changes at Red Bluff Diversion Dam after 1994 preclude the ability to collect comparable post-baseline data for this taxon.

b Mid-water trawl index for young-of-the-year American shad in the Sacramento-San Joaquin River Delta and San Pablo and Suisun bays, 1992-

2010.

c Estimated abundance of adult striped bass in the Central Valley’s anadromous waters, 1992-2010. Estimates for 2007, 2008, 2009, and 2010 are 

preliminary and subject to change. Years with missing data is due to CDFG survey frequency which is based upon funding.

d Estimated abundance of green sturgeon >40 inches in total length, 1992-2009. Estimates for 2006, 2007, 2008, and 2009 are preliminary and 

subject to change. Years with missing data is due to CDFG survey frequency which is based upon funding.

e Estimated abundance of 15-year-old white sturgeon, 1992-2009. Estimates for 2006, 2007, 2008, and 2009 are preliminary and subject to 

change.
20 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Watershed

Total actions and 

evaluations in Final 

Restoration Plan

Actions and 

evaluations

completed to date

Actions and 

evaluations 

addressed in 

20112

% of actions 

and evaluations 

completed to date

American River 13 2 15

Antelope Creek 2 0 0

Battle Creek 12 8 67

Bear Creek 2 0 0

Bear River 8 0 0

Big Chico Creek 10 3 30

Butte Creek 39 32 82

Calaveras River 6 0 1 0

Central Valley-Wide 15 1 7

Clear Creek 7 5 71

Colusa Basin Drain 2 0 0

Cosumnes River 9 2 1 18

Cottonwood Creek 5 1 1 20

Cow Creek 4 0 0

Deer Creek 5 0 0

Elder Creek 2 0 0

Feather River 12 0 0

Merced River 8 0 0

Mill Creek 5 1 20

Miscellaneous Small 

Tributaries

 1 0 0

Mokelumne River 13 1 8

Ocean 3 0 0

Paynes Creek 2 0 0

Upper Mainstem 

Sacramento River

 22 8 1 36

Sacramento-San Joaquin 

Delta

 29 0 0

Mainstem San Joaquin 

River

 13 0 1 0

Stanislaus River 9 1 1 11

Stoney Creek 1 0 0

Thomes Creek 6 2 33

Tuolumne River 10 0 1 0

Yuba River 14 0 0

All Watersheds1 289 67 7 23

1

 Actions to be implemented CVP-wide via tools identified in AFRP Final Restoration Plan.

2

 Actions and evaluations addressed in 2011 have not yet been completed.

Table 3: Summary of Progress Towards Completing 289 Final Restoration Plan Actions and 

Evaluations by Watershed, FY 1992-2011
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

priority actions that are “time certain”,structural (53) 

and non-structural actions (75) (Table 4). 

FY 2011 ACCOMPLISHMENTS 

The AFRP obligated $6,192,000 from the Restoration 

Fund and $2,648,919 from Bay Delta Funds in FY 

2011. The AFRP continued progress toward the 

following actions and evaluations in the Sacramento 

and San Joaquin watersheds to enhance passage 

and habitat, and reduce loss of fish. Table 2 shows 

the average natural production by species since 

1992. Fish count data is presented up to 2010. The 

2011 data is not available until June 2012, but will be 

posted in the 2011 CAMP annual report

The Central Valley Chinook salmon (all races) natural 

production average from 1992-2010 was 410,790 

fish which dropped below the 1967-1991 baseline 

average Chinook salmon production of 411,297 as 

a result of the low returns of fall run fish in 2010 that 

totaled 102,821 fish (Table 2). Average Chinook 

salmon natural production for the period 1992-2010 

has exceeded the watershed doubling goal target on 

Clear, Butte, and Battle Creeks and is just below the 

goal on the Mokelumne River (Table 5). Substantial 

gains in fish populations have been observed 

where investment in flow and passage has occurred 

(Butte, Battle, and Clear Creeks). Clear Creek and 

the Mokelumne River have also had a substantial 

investment in habitat restoration. Winter-run natural 

production numbers had continued to trend upward 

since 1994 until the poor returns from the last four 

years (2007-2010). Spring-run numbers have trended 

upwards since 1991, but production was reduced in 

2008, 2009, and 2010. Fall-run natural production 

has decreased to the baseline levels due to the recent 

stock collapse observed in 2007-2010. Late fall-run 

production had increased greatly since the low period 

(1993-1997) but continued to decline in 2010. 

Table 2 shows the 1992-2010 average natural 

production and the annual natural production 

estimates by species since 1992 and Table 5 shows 

the 1992–2010 average natural production numbers 

of Chinook salmon in each watershed compared to 

the AFRP doubling goal targets. Insufficient data are

available to estimate natural production of steelhead 

in the Central Valley other than upstream of Red Bluff 

Diversion Dam. Operational changes at Red Bluff 

Diversion Dam after 1994 preclude the ability to 

collect comparable post-baseline data for this taxon. 

Monitoring data for white sturgeon in San Pablo and 

Suisun bays are available for eleven years between 

Watershed 53 Structural Actions 75 Non-structural Actions

Number of structural 

actions completed 

in FY 2011*

Number of structural 

actions completed 

since 1992

Number of 

non-structural actions 

completed in 

FY 2011*

Number of 

non-structural actions 

completed since 1992

American River 1 1

Battle Creek 3 2

Big Chico Creek 1 1

Butte Creek 13 17

Clear Creek 1

Cosumnes River 1

Cottonwood Creek 1 1

Mill Creek 1

Stanislaus River 1

Thomes Creek 2

All Watersheds 21 25

* NOTE: Although non-structural actions were not completed in FY 2011, work continued on 17 watersheds throughout the 

Central Valley.

Table 4: Summary of Progress Towards 128 High and Medium Priority Actions Final 

Restoration Plan with End Points (53 Structural, 75 Non-Structural), FY 2011 and 

1992-2011
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Watershed Species Doubling Goal Target

1992-2010 Average 

Natural Production 

Numbers Percent of Target

American River* Fall-Run 160,000 109,438 68.4

Antelope Creek Fall-Run 720 0 0

Battle Creek* Fall-Run 10,000 17,953 179.5

Bear River Fall-Run 450 N/A N/A

Big Chico Creek Fall-Run 800 N/A N/A

Butte Creek Fall-Run 1,500 2,459 163.9

Clear Creek Fall-Run 7,100 10,890 153.4

Cosumnes River Fall-Run 3,300 793 24.0

Cottonwood Creek Fall-Run 5,900 1,548 26.2

Cow Creek Fall-Run 4,600 1,825 39.7

Deer Creek Fall-Run 1,500 849 56.6 

Feather River* Fall-Run 170,000 93,423 55.0

Merced River* Fall-Run 18,000 6,838 38.0

Mill Creek Fall-Run 4,200 1,908 45.4

Miscellaneous Creeks Fall-Run 1,100 78 7.1

Mokelumne River* Fall-Run 9,300 7,990 85.9

Paynes Creek Fall-Run 330 N/A N/A

Sacramento River Fall-Run 230,000 75,404 32.8

Stanislaus River Fall-Run 22,000 5,325 24.2

Tuolumne River Fall-Run 38,000 7,181 18.9

Yuba River Fall-Run 66,000 32,693 49.5

Central Valley Wide Fall-Run 750,000 372,244 49.6

Battle Creek* Late-fall-Run 550 676 122.9

Sacramento River Late-fall-Run 68,000 18,691 27.5

Central Valley Wide Late-fall-Run 68,000 18,383 27.0

Butte Creek Spring-Run 2,000 10,013 500.7

Deer Creek Spring-Run 6,500 2,100 32.3

Mill Creek Spring-Run 4,400 1,229 27.9

Sacramento River Spring-Run 59,000 749 1.3

Central Valley Wide Spring-Run 68,000 14,091 20.7

Calaveras River Winter-Run 2,200 0 0

Sacramento River* Winter-Run 110,000 6,578 6.0

Central Valley Wide Winter-Run 110,000 6,578 6.0

TOTAL All races 990,000 411,297 41.6

Table 5: Average Natural Production of Anadromous Fish in Each Watershed Compared to 

the Anadromous Fish Restoration Program Doubling Goal Targets, 1992-2010
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

1992 and 2009. In the seven years when 15-year-old

white sturgeon abundance estimates are considered to 

be final and not subject to revision (i.e., between 1993 

and 2005), the AFRP production target for this species 

was met once. In the four years when white sturgeon

estimates are considered to be provisional (i.e., 

2006, 2007, 2008, and 2009), the AFRP production 

target for 15-year-old white sturgeon was not met. 

Monitoring data for green sturgeon >40 inches (total 

length) in San Pablo and Suisun bays are available 

for ten years between 1992 and 2009. In the six

years when green sturgeon abundance estimates 

are considered to be final and not subject to revision 

(i.e., between 1993 and 2005), the AFRP production 

target for this species was met twice. In the four years

when green sturgeon estimates are considered to be 

provisional (i.e., 2006, 2007, 2008, and 2009), the 

AFRP production target for this species was also met 

twice. The midwater trawl index for juvenile American 

shad in the Sacramento-San Joaquin River Delta 

and San Pablo and Suisun bays suggests the AFRP 

production target for this species was met in three 

of 19 years between 1992 and 2010. The 2010 

midwater trawl index for this species (683) increased 

slightly from 2009 (624), but the 2010 index was 

markedly below the 1967-1991 baseline average 

of 2,129 shad and the AFRP production target of 

4,300 shad. Monitoring of legal-size striped bass in 

the Central Valley’s anadromous waters occurred in 

14 years between 1992 and 2010. In the 10 years

when legal-size striped bass abundance estimates 

are considered to be final and not subject to revision 

(i.e., between 1992 and 2005), the AFRP production 

target for this species was never met. In four years

when legal-size striped bass abundance estimates are 

considered to be provisional (2007,2008, 2009, and 

2010), the AFRP production target for this species was 

also not met. 

About 23% of all Restoration Plan actions and 

evaluations (289) have been completed in the 1992 

to 2011 time period (Table 3). Of the 128 time certain 

high and medium priority actions, forty-six (36%) have 

been completed since 1992 and one structural action 

was completed in 2011 (Table 4). Although nonstructural actions were not completed in FY 2011, work 

continued on 17 watersheds throughout the Central 

Valley. The AFRP continued progress toward the 

following actions and evaluations in the Sacramento 

and San Joaquin watersheds to enhance passage and 

habitat, and reduce loss of fish. 

Accomplishments in the Sacramento 

Basin

American River - Spawning and side channel habitat 

that were restored in 2010 were enhanced in 2011 

to improve the project design (FRP Action 5). Due to 

high flows, alternative scenarios have been developed 

to allow the installation of 3,000 to 8,000 cubic 

yards of gravel for spawning and 2,000 cubic yards 

of cobble to enhance flow into the side channel. 

Additionally, culled orchard trees are being purchased 

for installation in 2012 as instream woody habitat to 

improve the growth and survival of rearing juvenile 

fish.

Antelope Creek – The Juvenile Fish Passage 

Improvement Project at Edwards Diversion Dam (FRP

Action 1) will prevent out-migrating salmonids from 

becoming entrained in the two diversion canals. In

2011, the Tehama County Resource Conservation 

District completed an alternatives analysis for juvenile 

fish passage. Alternative selection and construction is 

expected to begin in 2012. 

The Antelope Creek Crossing Repair Project in the 

Tehama Wildlife Area (FRP Action 1) will remove 

a road crossing that is a barrier to spring- and fallrun Chinook salmon during dry years. Construction 

began in 2011 and will be complete in 2012. Once 

completed, the project will improve passage to 13 

miles of spawning and holding habitat.

Battle Creek –The fish screen and ladder construction 

at the Eagle Canyon and North Battle Creek Feeder 

sites was completed in 2011. Construction of the 

Inskip powerhouse tailrace connector and bypass

began in 2011 and is planned to be completed by late 

2012. Once current and planned 2012 contracts are 

completed, the project will improve flows and passage 

to 10 miles of spawning habitat (FRP Actions 2,6, and 

7). This project is being funded by CALFED, USBR, 

and PG&E.

Bear River – AFRP completed a report in 2011 

assessing the temperature data collected in 2010 

at six locations in Dry Creek, a tributary to the Bear 
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

River. Results suggest temperatures may be too 

warm in some locations to support over-summering 

steelhead, but future work may involve investigation of 

temperature refugia. Beale Air Force Base staff found 

an adult Chinook salmon in lower Dry Creek. Habitat 

restoration targeting fall-run Chinook salmon which 

typically do not over-summer may be warranted. 

Big Chico Creek–In FY 2011, the Sierra Nevada

Brewing Company pledged $200,000 towards the 

Iron Canyon Fish Ladder Project (FRP Action 2) and

NMFS issued the Biological Opinion. Completion 

of the new passage facility will provide access to an 

estimated 8 miles of quality spring run Chinook salmon 

habitat.

Cottonwood Creek –The Anderson-Cottonwood 

Irrigation District (ACID) siphon had become expose

once again in Cottonwood Creek and posed a 

passage problem for adult salmonids. Construction 

of the Cottonwood Creek ACID Siphon Project (FRP

Action 2) to alleviate this barrier was completed in 

November 2010. This project improved access to 

30 miles of spawning habitat for fall- and spring run 

Chinook salmon and Central Valley steelhead.

Surveys were conducted in 2011 to assist with the 

National Environmental Policy Act (NEPA) effects 

analysis on the Nonnative Invasive Plant Management

and Control Project (FRP Action 5) within the riparian 

corridor of Cottonwood Creek. Project implementation 

is anticipated to begin in 2012.

The Cottonwood Creek Geomorphological Analysis 

Project (FRP Action 1) was funded in FY09 to develop 

a sediment budget and assist in determining the 

cause of streambed instability. The study is to include 

analyses of geomorphological data from 1939 to 

present; quantify spatial and temporal characteristics 

of sediment supply, storage, and transport in the 

system; and to identify the effects of sediment transport 

dynamics on perceived channel and watershed 

changes. In 2011, additional funds were added

for continued flow and turbidity data collection on 

current sites/gages and for new collection sites to be 

monitored during the 2011/2012 water year.

Cow Creek – In 2011, a habitat survey above a

barrier in Cow Creek was completed for fall-run 

Chinook salmon and steelhead. Meetings with 

stakeholders to develop design alternatives for a 

fishway were also initiated. While design issues 

continue to be worked out, environmental compliance 

documents for NEPA and CEQA are anticipated to 

be completed by 2012. This project will open up 10 

miles of historic habitat to fall-run Chinook salmon and 

steelhead (Action 3).

FY11 funds were also awarded to complete a riparian 

habitat assessment and determine riparian restoration 

priorities (Action 4).

An anadromous fish passage barrier assessment was 

funded on July 2011. This assessment will inventory, 

classify, map, and prioritize barriers for remediation to 

restore access to 85 miles of anadromous fish habitat. 

The project will create a database and GIS layers

for agencies and stakeholders to use in addressing 

passage and screening issues related to man-made 

barriers and diversions.

Feather River – Monitoring activities targeting North 

American green sturgeon, which is listed as threatened 

under the Endangered Species Act, continued in the 

Feather and Yuba rivers in FY11. Future work may 

include additional video surveys and egg collection to 

verify spawning. Reports on sturgeon habitat surveys/

detection methodology and the 2011 observations 

were finalized. 

Mill Creek – In July 2011, the Mill Creek fish passage

assessment and restoration project was awarded 

(Evaluation 1). This project will assess and design 

any required remediation to improve fish passage 

for juvenile and adult salmonids at the two diversion 

dams and exposed siphon in the lower Mill Creek 

watershed. FY11 funds were also awarded to 

complete a riparian habitat assessment and determine 

riparian restoration priorities (FRP Action 4). 

Yuba River –Environmental documents were 

developed in 2011 to restore a 5-acre riparian site 

located on Hammon Bar (Evaluation 4). The project 

will plant cottonwood and willow pole cuttings within 

the Yuba River floodplain. This pilot project is intended 

to flood periodically under moderate flows and thus 

provide juvenile salmonids with improved rearing 

habitat.

Vaki Riverwatcher systems continue to be operated on 

the north and south fish ladders at Daguerre Point Dam 
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

in the lower Yuba River. The collection of fish passage 

data continues to improve understanding about the 

timing, abundance, population trends, and response 

to changing flow and temperature conditions of adult 

spring and fall-run Chinook salmon and steelhead. 

Data collected on steelhead has become much more 

reliable due to the installation of newer/improved 

equipment. Reports assessing the 2007-08 and 

2008-09 data were finalized. 

Accomplishments in the San Joaquin 

Basin

Calaveras River – The Budiselich Flashboard Dam 

boulder weir retrofit was completed this year and 

construction initiated on September 7th, 2011 and 

completed on October 1, 2011. This project restored 

access to about 10 miles of habitat (FRP Action 3). 

Cosumnes River – Post-project monitoring for the 

Cosumnes River Passage Improvement Project was

completed for 2011 and will continue in 2012. This 

project improved fish passage at Rooney Dam 

and restored access to about 10 miles of habitat 

(Evaluation 2). 

Additionally, AFRP provided FY11 funding to develop 

final designs, planning, and permitting to re-connect 

sloughs and floodplains within the Cosumnes River 

Preserve. One site, Cougar Wetlands, has been 

surveyed and a conceptual design to restore 80-85 

acres within three historic sloughs in the Delta has 

been developed (Delta Evaluations 4 and 6).

Merced River – AFRP staff developed a new 

agreement for rotary screw trap monitoring of 

outmigrant juvenile salmon. Outreach, planning, 

designs, and permitting for three different floodplain 

and channel restoration projects (FRP Action 3) 

were initiated in 2010 and continued through 

2011. The flow parameters, topographic surveys, 

benthic macro-invertebrate sampling, and substrate 

quality assessments were completed for all three 

floodplain and channel restoration projects this 

year. Construction activities on the Merced River 

Ranch Project included placement of approximately 

28,000 cubic yards of material for floodplain and 

rearing habitat. Once completed, the Merced River 

Ranch Floodplain Enhancement Project will restore 

up to 6 acres of riparian floodplain and 1.23 miles of 

spawning habitat. 

The AFRP continued to participate in the FERC 

proceedings for the Merced Falls (P-2467) and 

Merced River Hydroelectric (P-2179) Projects (Actions 

1 and 2; Evaluations 1 and 3). AFRP participated 

in multiple relicensing meetings in FY 11. Staff 

provided study proposals for a steelhead population 

assessment, egg viability/survival, and provided 

detailed comments on study plans for channel 

armoring, IFIM, and egg viability  AFRP is activel

participating in the Merced River Technical Advisory 

Committee and developing ongoing partnerships with 

numerous stakeholders in the watershed. 

Mokelumne River – AFRP purchased and placed 

6,557 tons of spawning gravel for the Mokelumne 

River Spawning Habitat Improvement Project (FRP

Actions 2 and 7). This project area is rigorously 

characterized and monitored each year for spawning 

use, bed form and function and provides a foundation 

project for the Spawning Habitat Integrated

Rehabilitation Approach (SHIRA). The final report will

be available after the project is completed in 2012.

In FY2011, AFRP staff worked with the EBMUD and

other signatories of the Lower Mokelumne Joint 

Settlement Agreement to adaptively manage the 

system and coordinate fall pulse flows (40,000 acre 

feet) with Delta Cross Channel (DCC) operations in an 

effort to improve adult Chinook salmon returns (Delta 

Evaluation 5). In 2011, high water conditions allowed

for spring pulse flows of 43,000 acre feet that was 

provided to assist outmigrating juvenile salmon and 

steelhead (Action 1 and Evaluation 1).

San Joaquin River – AFRP staff partnered with the 

California Department of Fish and Game (CDFG) 

to install VEMCO acoustic receivers in the San 

Joaquin River and continue an annual white sturgeon 

population assessment. Also, the AFRP documented 

spawning of white sturgeon in the San Joaquin River 

and partnered with USGS to map habitat-related 

physical characteristics along the San Joaquin River.

Stanislaus River – FY 2011 accomplishments 

included the collection of both juvenile and adult 

passage data via rotary screw trapping (juveniles) and 
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

a fish counting weir (adults) operated in partnership 

with Tri-Dam. Phase 2 of a Chinook salmon migration 

study was completed this year. AFRP is partnering with 

CDFG and Cramer Fish Sciences to implant acoustic 

transmitters in O. mykiss captured in screw traps or 

other sampling activities to evaluate outmigration and 

survival. These studies assist with evaluating benefits 

resulting from habitat restoration actions. The final 

permitting was completed in 2011for Honolulu Bar 

and Lancaster Road floodplain and side-channel 

enhancement projects (FRP Action 2). Construction at 

Lancaster Road was completed, and Honolulu Bar was 

delayed by high-water conditions until next summer. 

These projects were designed to increase juvenile 

salmonid rearing habitat and decrease predation. The 

Lancaster Road Project restored 640 feet of riparian 

side channel habitat. The Honolulu Bar Project will 

restore 2.47 acres of riparian floodplain, create 0.7 

acres of new floodplain, add 8,100 cubic yards of 

clean spawning gravel to the river, and restore 485 

feet of side-channel habitat.

Tuolumne River – The Bobcat Flat Restoration Project 

continued to restore spawning, rearing and floodplain 

habitats in the Tuolumne River (FRP Action 2). All 

environmental compliance requirements were 

completed in FY 2011. Avian and reptile surveys 

were completed this year. Phase 2 of the Bobcat Flat 

Restoration Project was implemented and involved 

recontouring 8 acres of highly disturbed floodplain 

in order to restore about 1.6 miles of fall run Chinook 

salmon and Central Valley steelhead spawning and 

rearing habitat.

Stanislaus River Side Channel Restoration Project at Lancaster Road, Post Construction.
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “other” & (b)(  

FISHERIES

The Trinity River Restoration Program (TRRP) is 

dedicated to the improvement of anadromous fishery 

resources in the Trinity River Basin. The program uses 

two authorities: CVPIA section 3406 (b)(1) “other” for

river restoration and CVPIA section 3406 (b)(23) for

delivering flows.

The Trinity River Mainstem Fishery Restoration Final 

Environmental Impact Statement (FEIS) completed i

October 2000, and the Record of Decision (ROD), 

signed on December 19, 2000, established a 

comprehensive science-based adaptive management 

program to restore the fishery resources of the Trinity 

River. The 2009 Master Environmental Impact Report

(Master EIR) on channel rehabilitation and sediment

management for remaining phase 1 and phase 2 

sites established the regulatory requirements for 

implementing physical river work required by the ROD. 

The program is based upon the goal of restoring the 

naturally produced anadromous fishery resources of 

the Trinity River by restoring the attributes of a healthy, 

alluvial river system through implementing variable 

annual instream flows, physical channel rehabilitation, 

sediment management, watershed rehabilitation and 

floodplain infrastructure improvements. Together, 

these actions will increase habitats for all life stages of 

anadromous salmonids, increase juvenile production 

and lead to increased spawning escapement and 

harvest opportunities of dependent fisheries. Since 

the ROD was signed, the TRRP has focused its physical 

restoration activities—such as gravel placement and 

channel rehabilitation activities—on the upper 40 

miles1 of the Trinity River between Lewiston Dam and 

1 “ISSUE PAPER FOR THE TRINITY MANAGEMENT COUNCIL, Is t

a Causal Link Between Restoration Activities in the South Fork Trinity River 

and other Tributaries and the Trinity River Diversion of the CVP.” This issue 

paper discusses the reasoning behind focusing restoration activities on 

the upper forty miles of the Trinity River.

the confluence with the North Fork of the Trinity River. 

Other restoration activities such as flow releases and 

sediment transportation benefit the entire riverine 

system.

PERFORMANCE MEASURES

The overall success of the program is gauged by 

naturally produced spawner escapement numbers 

relative to the goal (target) set for each species, 

and contributions to dependent tribal and non-tribal 

fisheries. Annual targets are found in Table 6. To 

achieve this overall goal, the program implements 

actions in several key areas that support the 

establishment of a healthy riverine system. Actions 

include scheduling annual flow of water, placement 

of coarse sediment, reduction of fine sediment 

delivery from watersheds by implementing watershed 

rehabilitation activities and physical channel 

restoration projects. 

Trinity River Restoration 

Program

 3406 (b)(1) “Other” & (b)(23)

Wheel Gulch restoration site.
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Flows – The program releases between 369,000 

and 815,000 AF each year, in accordance with the 

ROD. The annual volume target and peak flow varies 

according to the water year type. 

Placement of coarse sediment – The program 

may place up to 10,000 CY, on average, of coarse 

sediment annually. 

Fine sediment delivery and storage – The 

program aims to reduce fine sediment delivery from 

tributary watersheds by 10,000 to 20,000 CY 

annually. Additionally, the goal for fine sediment 

management is to transport as much or more fine 

sediment downstream as is delivered to the upper 

river from tributary watersheds to reduce in-channel 

storage.

Channel rehabilitation – The goal of the channel 

rehabilitation component of the program is to restore 

functioning alluvial river attributes and increase 

salmonid freshwater habitat. The ROD calls for 44 

bank rehabilitation projects and 3 side channels, 

which combine to make 47 sites. Channel restoration 

progress is currently measured by the number of 

completed sites. The final measure of the success 

of channel rehabilitation projects will be their 

effectiveness of promoting a dynamic alluvial river 

in conjunction with high flows and coarse sediment 

augmentation to increase salmonid habitat and 

restore the Trinity River fishery resources. This is 

being evaluated through the Program’s adaptive 

management process.

Other - In addition to the action oriented performance

measures listed above, the TRRP has developed 

performance measure documents that provide 

information pertaining to key metrics that are used to 

evaluate status and trends of these parameters. These 

Include: Temperature Target Performance; Chinook

and Coho Salmon Rearing Habitat; Abundance 

of Naturally Produced Juvenile Chinook Salmon; 

Spawning Escapement of Naturally Produced 

Salmonids; Proportion of Natural Origin Salmonids 

Contributing to Total In-River Run; Distribution

of Natural-Origin Chinook Salmon Spawners; 

Abundance Patterns Over Time of Riverine Birds; 

Abundance Patterns Over Time for Riparian Birds,; and 

Comparison of Turtles on the South Fork Trinity and 

Mainstem Trinity. These documents can be found at: 

www.trrp.net/?page_id=490

FY 2011 ACCOMPLISHMENTS 

In FY 2011, the Trinity River Restoration Program

obligated $3,503,949 from the Water & Related 

Resources Fund (b)(23), $8,655,938 from the Water 

& Related Resources Fund (b)(1) “other”, Restoration 

Funds of $988,819, and American Recovery and 

Reinvestment Act (ARRA) funding was $41,296.

Naturally Produced Adult Spawner Escapement2

Trinity River Hatchery Produced– Adult 

Spawner Escapement3

Fall 

chinook4

Spring 

Chinook5

Fall 

Steelhead6 Coho7

Fall 

Chinook4

Spring 

Chinook5

Fall 

Steelhead6 Coho7

Target 62,000 6,000 40,000 1,400 9,000 3,000 10,000 2,100

2010 20,876 4,477 3,811 817 8,953 3,880 4,640 5,852

Average 14,188 5,483 4,170 1,890 18,827 9,285 12,556 12,282

 

1

 Data compiled by DFG. Means are from 1992 to 2010 unless otherwise noted.

2

 Estimates of naturally-produced adult salmonid spawner escapement for combined natural and hatchery spawning areas.

3 Estimates of hatchery-produced adult salmonid spawner escapement for combined natural and hatchery spawning areas.

4

 Fall Chinook estimates upstream of Willow Creek weir 1992 - 2010. Trinity River Basin estimate for 2001 - 2010 (assumes no 

straying of hatchery produced spawner escapement downstream of Willow Creek weir).

5

 Spring Chinook estimates upstream of Junction City weir combined with dive counts for the South Fork Trinity River and 

miscellaneous tributaries. Data were not collected in 1995 due to funding constraints.

6

 Fall-run steelhead estimates upstream of Willow Creek weir for all years of data collected. Does not include summer- or winterrun steelhead estimates. Data were not collected from 1997 to 2001 due to funding constraints.

7

 Coho estimates upstream of Willow Creek weir for all years after 1997

Table 6: FY 2010 Salmonid Production, Natural vs. Hatchery 
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “other” & (b)(  

FISHERIES

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2011

Fiscal 

Year Water Year Type ROD Flow Target ROD Flow Provided* Peak Releases (cfs)

2006 Extremely wet 815,000 AF 809,900 AF 10,100

2007 Dry 453,000 AF 453,700 AF 4,750

2008 Normal 647,000 AF 648,700 AF 6,470

2009 Dry 453,000 AF 445,500 AF 4,410

2010 Normal 647,000 AF 656,700 AF 6,840

2011 Wet 701,000 AF 721,800 AF 11,600

 * Computed flow volume ± 5% based on stream flow measurement accuracy.

Flows – Water volume peak flow was modified to an 

11,600 cfs release to facilitate geomorphic processes, 

especially at newly constructed channel rehabilitation 

sites. The ROD prescribed peak flow for a wet water 

year is 8,500 cfs (see Table 7 for ROD flows).

Course Gravel and Channel Rehabilitation – As 

shown in Table 8, the program added 5,300 CY 

of coarse gravel to the river during high flows this 

year and completed the first of its phase 2 channel 

rehabilitation projects at Wheel Gulch (see Table 9). 

Watershed projects implemented in FY 2011 will 

keep approximately 9,600 CY of fine sediment out 

of the mainstem. In addition, the condition of the bed

indicates that more fine sediment was transported 

downstream than came into the upper 40 miles 

of the Trinity River. The program also continued 

planning and engineering for the next four channel 

rehabilitation projects. 

Monitoring and Assessment – approximately $4 

million was obligated in FY 2011 to include stream 

gaging, sediment transport, course and fine sediment 

budgets, smolt outmigration population size and 

timing, adult spawning escapement separated by 

natural and hatchery, sport and tribal harvest, system 

wide habitat assessment, evaluation of habitat 

produced through construction, riparian vegetation 

recruitment and encroachment and system wide 

bird abundance . Results from salmon production 

monitoring is below in Table 6. 

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2011

Fiscal 

Year Gravel Augmentation Location Gravel * (CY) Total per Year* (CY)

2003 Cableway 2,000 2,000

2006 Hatchery 1,600 1,600

2007 Hatchery 4,300 4,300

2008

High Flow Injections 2,300

12,300 Lewiston-Dark Gulch 10,000

2009

High Flow Injections 2,300

 8,000

Sawmill 5,700

2010

High Flow Injections 3,100

13,500

Lowden Ranch Area and Reading Creek 10,400

2011 High Flow Injections 5,300 5,300

Total 47,000

 * Volume for mobile coarse gravel only. Reported volumes do not included oversized gravel or structural gravel to build 

permanent in-river features.
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Table 9: Rehabilitation Site Construction Summary, 2005-2011 

Fiscal 

Year Rehabilitation Site

Number 

of Sites Earth-work (CY)

Feet of Large 

Wood Habitat 

Structures

River 

Miles

Acres 

Treated

2005 Hocker Flat (complete) 1 83,000 0 1.0 26

2006 Canyon Creek Sites 

(complete)

 4 91,000 100 1.7 40

2007 Indian Creek Sites 

(complete)

 3 77,800 200 2.8 31

2008 Lewiston and Dark 

Gulch Sites (complete)

 8 56,900 200 3.7 42

2009 Sawmill and Steel 

Bridge Day Use* 

(complete)

 2 87,750 260 0.8 25

2010 Lowden, Trinity House 

Gulch, Reading Creek 

 5 202,600 300 2.4 36

2011 Wheel Gulch 

(complete)

 1 48,000 200 0.3 7

Total 24 647,050 1,260 12.70 207

* The No-Action alternative was chosen for the Steel Bridge Day Use Project Site.

Spring Chinook salmon spawning in the mainstem Trinity River
DEDICATED 800,000 ACRE-FEET PROJECT YIELD 3406 (b)(2  

FISHERIES

CVPIA authorizes a portion of the CVP project yield

to be dedicated and managed for the benefit of 

fish and other wildlife. Interior has the responsibility

to annually dedicate and manage up to 800,000 

AF of CVP (b)(2) water for fish, wildlife and habitat 

restoration purposes. This water includes both CVP 

releases and decreased CVP export pumping, relative 

to a hypothetical pre-CVPIA baseline operation

(base case). This accounting is applied specifically to 

changes in operations on the American River (Nimbus 

Dam), Sacramento River (Keswick Dam), Stanislaus 

River (Goodwin Dam), Clear Creek (Whiskeytown 

Dam) and the Delta pumps (Jones Pumping Plant). 

The management of (b)(2) water is partially informed 

by the Anadromous Fish Restoration Plan (AFRP) 

developed per Section (b)(1), and the results of 

Instream Flow Incremental Methodology (IF

studies, undertaken as part of Section (b)(1)(B), which 

identify optimal flow, temperature needs, and timing 

for the life stages of anadromous fish.

The Dedicated Yield Program (DYP) actions affecting 

fish fall into the following categories: 

•	Instream flow augmentations on CVP-controlled

streams intended to protect salmon and 

steelhead, as well as contribute toward meeting 

Anadromous Fish Restoration Program (AFRP) 

Final Restoration Plan flow objectives

•	Increased releases from Goodwin Reservoir

to help meet the Water Quality Control Plan 

(WQCP) requirements for San Joaquin River 

flows at Vernalis for fish and wildlife standards

•	Increased releases from Keswick and/or

Nimbus reservoirs to help meet the WQCP fish 

and wildlife standards

•	Export reductions at the CVP Jones pumps to 

protect at-risk fish species, notably salmon, 

steelhead and delta smelt, and to help meet the 

WQCP Delta standards

PERFORMANCE MEASURES

Annual contribution – Reclamation annually 

contributes up to 800,000 AF of water from CVP 

facilities. In dry years, the target may be reduced to

700,000 AF. In critically dry years, the target may be

reduced to 600,000 AF.

Contribution to fisheries habitat goal – The 

800,000 AF of water contributes towards the 

1,000,000 AF fishery habitat goal. The Section (b)

(3) Instream Water Acquisition Program contributes

the balance, up to 200,000 AF, towards this goal, as 

described in the CVPIA record of decision (ROD)

FY 2011 ACCOMPLISHMENTS 

The program obligated $698,000 from the 

Restoration Fund in FY 2011. 

The full 800,000 AF of (b)(2) water was available for 

fish actions in water year 2011. Table 10 presents the 

historic allocation and use of (b)(2) water. Table 11 

summarizes how 348,800 AF of (b)(2) water was used 

in 2011 by location for fish and wildlife purposes. The 

remaining 451,200 AF of unused water remained in 

system for other project purposes.

Monies for this program activity fund real-time fish 

monitoring which informs when and where fish actions 

should be taken. On a weekly basis, fishery biologists 

from the Sacramento, San Joaquin and Delta regions 

report on fish movements to a B2 Interagency Team

(Team). The Team, including fishery biologists from 

Dedicated 800,000 acre-feet 

Project Yield

 3406 (b)(2)
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

FWS, USBR, NOAA, CDFG, and DWR, evaluate 

the data and collaboratively decide where to apply 

CVPIA (b)(2) water. Interior provides detaile

accounting of (b)(2) fish actions at www.usbr.gov/mp/

cvo.

Table 10: Allocation Target and Use of (b)(2) Water, 2001-2011

Allocation of (b)(2) Water Use of (b)(2) Water

Year

Water Year 

Type*

(b)(2) 

Allocation Target

(acre-feet)

Allocated

Flow**

(acre-feet)

Unused***

(acre-feet)

Banked

(acre-feet)

2001 Dry 800,000 798,000

2002 Dry 800,000 793,000

2003 Above Normal 800,000 796,000

2004 Below Normal 800,000 800,000

2005 Above Normal 800,000 672,000 128,000

2006 Wet 800,000 422,000 183,000 195,000

2007 Dry 800,000 798,000

2008 Critical 600,000 600,000

2009 Dry 600,000 600,000

2010 Below Normal 800,000 800,000

2011 Wet 800,000 348,800 451,200

* Water Year Type is based on the Sacramento Valley Index.

** Total water volume accounted for as (b)(2)

*** Section 3406 (b)(2)(D): If the quantity of water dedicated under this paragraph, or any portion thereof, is not needed for the 

purposes of this section, based on a finding by the Secretary, the Secretary is authorized to make such water available for 

other project purposes.

River Action Timeframe Results

American None None WY 2011 was classified as wet in the Sacramento 

River basin. No (b)(2) actions taken.

Clear Creek WY 2011 was classified as wet in 

the Sacramento River basin. (b)

(2) water was used to augment 

base case flows

October 1, 2010 –

September 30, 

2011

Contributed to AFRP Final Restoration Plan flow 

objectives and improved instream conditions for 

fall-run Chinook, spring-run Chinook and steelhead 

during spawning, incubation, rearing and downstream 

migration.

(b)(2) water was used to provide 

short pulse flow.

May 2011 Contributed to AFRP Final Restoration Plan flow 

objectives and provided pulse flow to attract adult 

spring-run Chinook salmon to suitable spawning 

areas.

Sacramento (b)(2) water used to augment 

would-be base flows to maintain 

3800 cfs

February 2011 Contributed toward AFRP Final Restoration Plan flow 

objectives and improved instream conditions for late 

fall- and fall-run Chinook spawning and emergence.

Stanislaus (b)(2) water used to augment 

base case flows

October 2010 Provided pulse flow to attract adult fall-run Chinook 

salmon to suitable spawning area

(b)(2) water used to augment 

base case flows

October 2010 –

March 2011

Contributed toward AFRP Final Restoration Plan flow 

objectives and improved instream conditions for fallrun Chinook and steelhead for spawning/rearing. 

CVP Jones 

Pumping 

Plant

Reduction in CVP exports 

accounted as (b)(2) water since 

sufficient assets were expected 

to be available to cover future 

primary purpose actions

March 2011 Compliance with NMFS Old and Middle River 

requirement

Federal exports were reduced 

pursuant to the NMFS BO. This 

year the reduction was accounted 

as a (b)(2) expenditure.

May 2011 Benefitted out-migrating salmon and steelhead 

smolts. Concurrent benefits to delta smelt.

Table 11: FY 2011 Use of (b)(2) Water by Location
DEDICATED 800,000 ACRE-FEET PROJECT YIELD 3406 (b)(2  

FISHERIES

Holding salmon in Clear Creek.
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

3406 (d)(2), Refuge Water Acquisition Program 

(Refuge WAP).

PERFORMANCE MEASURE

Acquire up to 200,000 AF per year to supplement the 

800,000 AF dedicated from CVP yield to meet the 

fisheries flow objective of 1,000,000 AF (per ROD, 

CVPIA Final PEIS, Jan 2001

FY 2011 ACCOMPLISHMENTS 

The Instream WAP obligated $6,799,000 from the

Restoration Fund and $1,404,887 from the State of 

California Cost Share Fund in FY 2011. The Instream

WAP used this funding to acquire a total of 38,500 AF 

in these areas:

•	12,500 AF for Merced River and Lower San 

Joaquin River pursuant to the VAMP/SJRA.

•	Completed final year of SJRA contract for the 

ability to use up to 110,000 AF for VAMP 

spring pulse flows. However, no additional 

flows were required in April and My 2011.

•	26,000 AF for Stanislaus and lower San 

Joaquin River flows, along with water quality 

and other authorized New Melones purposes. 

Table 12 shows the instream water acquisitions from 

1994-2011.

The Instream Water Acquisition Program (Instrea

WAP) acquires water to supplement the 800,000 

acre-feet (AF) of CVP yield that is dedicated to 

fisheries. The increased flows benefit numerous 

resident and anadromous fish species, but primarily 

benefit Central Valley Chinook salmon, the majority of 

salmon produced in California. At times, this species 

has accounted for up to 70% or more of the statewide 

commercial harvest. 

The Instream WAP primarily manages an agreement

with 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. The flows are 

used in support of the San Joaquin River Agreement 

(SJRA) and the Vernalis Adaptive Management 

Plan (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. In

support of the 2009 National Marine Fisheries 

Service (NMFS) Operations Criteria and Plan (OCAP) 

Biological Opinion, the VAMP program is currently 

funding studies to confirm the outmigration success of 

salmon smolts. The smolts are released upstream of 

Vernalis, CA and are recaptured in the western delta. 

Water acquisition for CVPIA-designated refuges and

wildlife management areas is discussed in Section 

Water Acquisition Program – 

Instream Water

 3406 (b)(3) & (g)
WATER ACQUISITION PROGRAM - INSTREAM WATER 3406 (b)(3) &   

FISHERIES

Table 12: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 

 1994-2011

Year AF Acquired

% of 200,000 

AF target

1994 76,441 38

1995 0 0

1996 16,161 8

1997 155,983 78

1998 80,000 40

1999 224,498 112

2000 108,880 54

2001 109,785 55

2002 68,105 34

2003 91,526 46

2004 98,211 49

2005 38,500 19 

2006 38,500 19

2007 114,645 57

2008 106,490 53

2009 38,500 19

2010 62,480 31

2011 38,500 19

Average 81,511 41
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

The Tracy (Jones) Pumping Plant’s six pumps, each 

capable of pumping 767 cfs into the Delta Mendota 

Canal, are powerful enough to alter stream flow in the 

Delta and the San Joaquin River Basin. This disorients 

migratory fish and draws them toward the pumps 

where they can become entrained, or trapped. 

To mitigate entrainment, the Tracy Fish Collection 

Facility (TFCF), located upstream of the pumping plant, 

collects migratory fish and transports them to the Delta 

where they can resume outmigration to the ocean. 

The focus of the (b)(4) program is to improve fish 

protection and salvage through development of new 

technologies. Ongoing monitoring of the program’s 

effectiveness helps define best practices that inform 

decision-making and long-term planning at Tracy and 

other South Delta facilities. 

PERFORMANCE MEASURES

The Tracy (Jones) Pumping Plant program (TPPP) 

develops and implements actions to mitigate impacts to 

fisheries, targeting the 23 actions included in The Tracy 

Fish Facility Improvement Program Plan, as shown in

Table 13.

FY 2011 ACCOMPLISHMENTS 

The program obligated $2.2 million from Water 

& Related Resources program for the Tracy Fish 

Collection Facility; and $15,000 from the Bay-Delta 

Program for the Two Gates Fish Demonstration Project.

Actions to Improve Tracy Fish 

Collection Facility 

The program continued engineering and biological 

assessments in support of Actions 17 and 18, which 

will improve the louver cleaner systems and allow the 

louvers to screen fish more efficiently. Also, continued 

to work on design details towards eventual completion 

of Action 19, which will result in the development of 

land to better Reclamation’s ability to conduct research 

onsite and improve fish protection at the TFCF. 

Conceptual design and options in support of Action 

20 were completed as well. Action 20 is intended to 

reduce fish predation, debris management, hydraulic 

control, louver screening, and fish transfer impacts 

through the construction of a new secondary screening 

and transfer system. Continued assessments were also 

conducted in support of Action 23

In addition to the 23 actions listed in Table 15, the

program also completed a number of studies that will 

improve fish capture and reintroduction capabilities. 

The studies include salvage efficiency tests for 

delta smelt, evaluation of predatory impacts within 

the secondary system of the TFCF, and obligated 

schooling of threadfin shad during simulated 

transportation. 

Some of these studies are related to specific RPA 

action items and some are included in the facility 

assessment program. The facility assessment program 

is needed in order to understand present day 

operational characteristics so as to have a baseline to 

compare improvements to and also figure out which 

technologies and concepts to apply to the eventual 

physical improvements.

Tracy (Jones) Pumping Plant

Program

 3406 (b)(4)
TRACY (JONES) PUMPING PLANT PROGRAM 3406 (b)(4) 3

FISHERIES

Actions Start Date Completion Date

 1 Implemented periodic predator removals 1992 “ongoing”

 2 Upgraded instrumentation at the TFCF 1992 1993

 3 Replaced high pressure utility pump with low pressure utility pump 1995 1996

 4 Epoxy coated recessed collection tanks 1997 1997

 5 Constructed aquaculture facility onsite 1997 2005

 6 Constructed extraction device for Chinese mitten crabs/debris removal 1998 1999

 7 Installed air system in recessed collection tanks 1999 1999

 8 Developed onsite laboratory for fish taxonomic work 1999 1999

 9 Added air system to fish haul trucks 2000 2000

10 Upgraded fish count area to accommodate DNA sampling & fish ID 2000 2000

11 Updated fish identification key for training of operators 2000 2000

12 Replaced worn (“leaky”) bypass transition boxes 2003 2004

13 Replaced fish transfer bucket with new/improved fish transfer bucket 2006 2008

14 Replaced fish haul trucks with new/improved fish haul trucks 2006 2008

15 Constructed new biological resources building 2006 2010

16 Replaced existing trash rack cleaner with new/improved trash rack cleaner 2006 2010

17 Replace primary louvers/cleaners with new primary louvers/cleaning 

system

2006 2017*

18 Replace secondary louver/cleaners with new secondary louvers/cleaning 

system

2006 2014*

19 Develop land onsite to improve ability to conduct research 

and operate the facility

2006 2018*

20 Construct new secondary screening and transfer system 2010 2016*

21 Construct new aquaculture facility onsite 2012 2020*

22 Automate velocity control pumps for the fish bypass system 2013 2014*

23 Construct third fish release site 2014 2016*

* Estimated Completion Date

Table 13: Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan 

Actions
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

The Contra Costa Canal is essential to the Contra 

Costa Water District, delivering water from the Delta 

to the district’s treatment facilities and raw-water 

customers. The canal is 48 miles long, starting at Rock 

Slough in East Contra Costa County and ending at the 

Terminal Reservoir in Martinez. Four pumping stations 

currently lift water 124 feet above sea level from 

Rock Slough, and then gravity propels the water to its 

terminus in Martinez. 

Contra Costa Pumping Plant No. 1 is located at the 

head of the Contra Costa Intake Channel. Without

adequate screening or alternative mitigation, the 

operation of the Contra Costa Pumping Plant No. 

1 results in fish mortality. In addition to the CVPI

mandate, the 1993 Los Vaqueros BO and the 2009 

NMFS OCAP BO require that a fish screen be built 

at Rock Slough. A screen, 320-feet in length, was 

designed to match the flow of the Contra Costa Canal 

Intake Channel at the Rock Slough Fish Screen and

to keep fish from entering the Contra Costa Canal 

intake. This will minimize the entrainment and loss 

of fish, fulfill legal requirements of the U.S. Fish and 

Wildlife Service’s Los Vaqueros Biological Opinion 

for the threatened Delta smelt, and complete Central 

Valley Project Improvement Act, Section 3406(b)(5)

requirements.

PERFORMANCE MEASURES

The Contra Costa program (CCP) mitigates fishery 

impacts with operational changes and installation of 

structures, including a fish screen. 

FY 2011 ACCOMPLISHMENTS 

The CCP obligated funding from a variety of sources: 

$2.4 million from the American Reinvestment and 

Recovery Act (ARRA), $13,396 from the Water & 

Related Resources Fund, and $4,622 from the BayDelta Fund. 

In 2011 the CCP finished the third and final

construction phase of the fish screen structure. Through 

the year the major components of the fish screen were 

assembled. In November (FY 2012) the fish screen

was substantially complete and operational.

Contra Costa Canal Pumping 

Plant

 3406 (b)(5)
CONTRA COSTA CANAL PUMPING PLANT 3406 (b)(5) 3

FISHERIES

Construction of the Rock Slough Fish Screen substantially complete and operational. This project is located where the Contra 

Costa Canal Intake Channel is diverted off Rock Slough.
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

The Red Bluff Diversion Dam (RBDD) is located on the 

Sacramento River about 2.5 miles southeast of the 

city of Red Bluff. The dam has 11 gates that, when 

partially closed, divert water to the Tehama-Colusa 

and Corning canals to provide water for farmers, the 

Sacramento National Wildlife Refuges (SNWR), and 

minor municipal and industrial uses. In the summer, the

dam creates a seasonal lake in a wide portion of the 

Sacramento River, attracting recreational users 

Construction of the dam has impaired the ability of 

Chinook salmon to reach historic spawning habitat. 

To address this impact, a number of operational 

modifications have been tried and tested since 1986 

when the gates were first raised to allow passage 

from December to April. By 1992, the winter-run 

population numbers had declined dramatically; an 

estimated 191 adults returned that year, resulting in 

winter-run Chinook being placed on the Endangered 

Species Act List. As a result the program began 

lifting the gates as an operational measure to 

promote species recovery. The gates were open for 

longer periods of time between 1992 and 1994, 

allowing winter-run population numbers to increase to 

approximately 20,000. 

Operation of the dam gates also blocks passage of 

green sturgeon during their spawning migrations. 

Green sturgeon in the Sacramento River were listed as 

threatened under the ESA in 2006.

The NMFS’ 1993 BO on the CVP/SWP operation 

required that the gates be raised September 15th to 

May 14th, beginning in 1994. The BO effectively 

moved the beginning date back from November 1 

to September 15th to encourage spawning activity 

Red Bluff Diversion Dam

 3406 (b)(10)

Concrete complete on the pumping plant in FY 2011. Looking from downstream to upstream.
RED BLUFF DIVERSION DAM 3406 (b)(10  

FISHERIES

further upstream and moved the ending date forward 

from April 30th to May 14th to reduce predation 

losses at the gates (NMFS 1993b, p. 54)

Until 2011, two temporary pumping plants allowed 

the gates to remain open for 10 months each year 

(September - June). Although gate operations 

enabled the fall-run Chinook populations to increase 

in numbers, the spring-run Chinook populations 

continued to be impacted. As a result, the 2009 

NMFS OCAP BO required the gates be raised yearround after 2011. The temporary pumping plant did 

not meet the capacity needs to deliver year-round 

irrigation supplies to local farmers. Therefore, the 

ability to meet the irrigation demand for 150,000 

acres of agricultural land in the Tehama-Colusa Canal 

Authority would be severely compromised, if the new 

facility is not completed by May of 2012. The longterm solution is the construction of a new permanent 

pumping plant that will allow the RBDD gates to 

remain open year-round, without affecting deliveries 

to water contractors and the Sacramento National 

Wildlife Refuge (SNWR).

PERFORMANCE MEASURES

The Red Bluff Program’s (RBP) current goals include 

passage of 80–100% of adult spring-run salmon, the 

run that continues to be significantly blocked. The RBP 

aims to achieve this target while maintaining water 

deliveries. This measure includes monitoring to confirm 

the successful passage of spring-run salmon above 

and below the dam.

Passage of 50-100% of adult green sturgeon is also 

targeted while maintaining water deliveries to SNWR 

and other water contractors. This measure includes 

monitoring to confirm the successful passage of green 

sturgeon above and below the dam. 

The last goal of the RBP is to develop capacity for 

conveyance of 115,000 acre-feet (AF) of refuge 

water to the SNWR Complex on the west side of the 

Sacramento River. This performance measure was 

met in 1999 when a siphon was installed on the GCID

Canal at Stony Creek to allow year-round deliveries. 

The new pumping plant will provide a backup to 

conveyance via GCID’s facilities

FY 2011 ACCOMPLISHMENTS 

In FY 2011, the RBP obligated funding from a variety

of sources:

•	$22,267,909 from Water and Related 

Resources Fund

•	$7,289,444 from the American Recovery & 

Reinvestment Act Fund

•	$2,704,647 from the State of California Cost 

Share Fund

Pumping Plant and Fish Screen 

Construction of the new, 2,500-cfs permanent 

pumping plant and fish screen progressed during FY 

2011: 

•	The Bridge, Siphon and Canal contract moved 

to being nearly complete in FY 2011 with 

the completion of the bridge and siphon. 

Significant progress was made on the canals 

and landfill closure that were part of this project.

•	The pumps and motors were fabricated and 

delivered to the project during FY 2011. They 

will be installed and tested by the Pumping 

Plant/Fish Screen Contractor.

•	The concrete work on the Pumping Plant was 

completed during FY 2011 and most of the 

forebay excavation and fish screen concrete 

work was completed. 

The Pumping Plant and Fish Screen are on schedule 

to deliver water to the Tehama Colusa Canal in May, 

2012.

Passage of Spring-Run Salmon

On June 15, 2011, the RBDD gates were lowered but 

were kept open a minimum of 18 inches to allow the 

safe passage of out-migrating adult green sturgeon. 

Two acoustically tagged adult green sturgeon 

successfully passed through and were subsequently 

detected downstream by mobile tracking and 

stationary receivers.

Based on latest gate operations of the facility, 

approximately 80% of adult spring-run Chinook 

achieved unimpeded upstream passage in FY 2011.
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Compliance with 2009 NMFS BO – The RBP 

continued green sturgeon studies, in compliance with 

the BO-required actions. In FY 2011, egg sampling

occurred over a 94-river-kilometer range between 

Jelly’s Ferry Bridge and Highway 32/Gianella Bridge. 

Preliminary results indicate that green sturgeon 

spawning occurred from early April to late June, and 

larvae are emerging from the spawning grounds 

between May and August.

Furthermore, spawning adults have been found 

to spawn in the tailrace of the dam in most years 

(including 2011) and, at times, in locations that are 

detrimental to the production of recruits due to RBDD 

operations and the physical disturbance (in terms of 

sediment) created by water flowing underneath RBDD 

gates. Finally, knowing the basic life history of this 

listed species in relation to current water resource 

management mandates (i.e., winter run temperature 

compliance targets), allows managers to better 

formulate recovery actions for this species in a highly 

regulated river system such as the Sacramento that has 

a number of ESA listed species to be concerned with 

presently and in the future.

Fish Screen with concrete placement and forebay excavation mostly complete in FY 2011.
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 4

FISHERIES

Clear Creek suffered widespread degradation through 

the 20th century due to several factors, including 

construction of McCormick-Saeltzer Dam in 1903, 

construction of Whiskeytown Dam in the 1960s, 

and aggregate and gold mining activities. These 

actions led to precipitous drops in Chinook salmon 

and steelhead spawning and juvenile production. In

order to reverse the trend, CVPIA is implementing

a restoration program to improve instream habitat, 

allowing greater spawning and rearing success.

PERFORMANCE MEASURES

The Clear Creek Restoration Program (CCRP) focuses 

on the following areas and uses the following goals 

to track progress: fish passage; erosion control; gravel 

placement (creation of spawning habitat); channel 

restoration; instream flow and temperature of flow 

releases. All of these goals are in support of the 

overall CCRP objective of restoring fish populations 

in Clear Creek, and increasing natural production, to 

meet the annual target of 7,100 for fall-run Chinook in 

Clear Creek. Although there is no doubling target for 

spring-run Chinook on Clear Creek, restoration actions 

will also help increase spring-run Chinook populations, 

contributing to the CVPIA’s Central Valley-wide goals

Fish Passage – The fish passage target was achieved 

in 2000, when McCormick-Saeltzer Dam was 

removed, opening 12 additional miles of habitat to fish 

passage. 

Clear Creek Restoration 

Program

 3406 (b)(12)

Sluicing (injecting a “slurry” of water and spawning gravel) into Clear Creek upstream of the Peltier Campground during a FY 

2011 gravel injection project where the site is inaccessible by dump truck
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Erosion Control – The erosion control target was 

achieved ahead of schedule. All feasible and costeffective erosion control projects initially identified 

were completed by 2001 and the necessity for further 

work will need to be determined. 

Gravel Placement (Creation of Spawning 

Habitat) – The CCRP goal is to replenish Clear 

Creek spawning habitat areas with approximately 

17,000 tons of gravel every year. Gravel placement 

contributes to the restoration of the 347,288 square 

feet of spawning habitat that existed before the 

construction of Whiskeytown Dam.

Channel Restoration – The CCRP is restoring 2 miles 

of stream channel to support successful spawning and 

rearing.

In-stream Flows and Temperature of Flow 

Releases – The CCRP provides instream flows, 

depending on hydrology and biological conditions, to 

ensure that flow volumes and temperature meet habitat 

needs for successful spawning and rearing. Using (b)

(2) water and coordinating with operators, the CCRP 

aims to provide water at 60°F June 1–September 15, 

and 56°F September 16–October. The goal is to 

meet these targets at least 98% of days, with no more 

than two consecutive days of releases when exceeding 

the temperature target. The timing of flows benefit 

both spring run and fall run Chinook but are especially 

important to spawning spring run Chinook as they 

can only spawn in water cold enough to sustain eggs 

through their incubation period. 

Since 1999, studies have been undertaken by CVPIA

and CALFED to develop channel maintenance 

flows, which are vital for providing and maintaining 

spawning and rearing habitat in Clear Creek. In

2008 FWS and CALFED contracted to facilitate a 

pilot re-operation of Whiskeytown reservoir to achieve 

the channel maintenance flow prescription. This 

Environmental Water Program prescription calls for the 

re-operation of Whiskeytown Dam, between March 

1 and May 15, to produce a Glory Hole spill event 

that results in a minimum target release of 3,250 cfs 

for a one-day duration. This event would occur seven 

times in a ten-year period. Flows of this magnitude 

and duration could reactivate fluvial geomorphic 

processes to re-create and maintain diverse instream 

and floodplain habitat required to support and recover 

aquatic and riparian species. This flow prescription is 

also required in the NMFS OCAP BO.

Monitoring and Adaptive Management – 

Although this is not a distinct goal for the CCRP, 

monitoring and adaptive management are important 

because these activities help the CCRP address limiting 

factors and achieve greater success in meeting its 

goals and RPAs.

FY 2011 ACCOMPLISHMENTS 

In FY 2011, the CCRP obligated $679,838 from the

Restoration Fund and $280,793 from the Water and 

Related Resources Fund.

Gravel Placement (Creation of Spawning 

Habitat) – A total of 10,000 tons of gravel was 

placed in Clear Creek in 2011 representing 58% of 

the annual target. More than 21,000 square feet of 

spawning habitat was created by the FY 2011 gravel 

placement projects.

•	Gravel was placed in five sites during 2011: 

below Whiskeytown Dam, below Dog Gulch 

Creek, Above Peltier Bridge, Paige Bar (below 

Peltier Bridge), and below NEED Camp 

(Guardian Rock site).

The second annual evaluation of spawning gravel 

implementation and monitoring was submitted to 

NMFS as a requirement under the OCAP BO. Studies 

in 2011 suggested that gravel sizes specification 

should be modified in future years to improve use 

by spring Chinook. The FWS and BOR began 

cooperatively developing a new specification that will 

be tested during FY 2012.

Channel Restoration – Phase 3C, the last phase 

of the restoration project, will be considered for 

implementation in future years. On-going analyses are 

expected to result in final recommendations by the end 

of FY 2013.

Instream Flows and Temperature of Flows – The 

CCRP met its goal of providing base flows of 200 cfs 

between October 1–May 31. In addition, two pulse

flows were provided during spring 2011 to help attract 

spring-run Chinook to Clear Creek. Although the 

spring-run population numbers continued to decline, 

and the numbers of spring-run Chinook (7) were low 
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 4

FISHERIES

Downstream of the Peltier Campground, a truck prepares to place gravel on bank of Clear Creek. The gravel is mobilized 

downstream during high flow events

in 2011, the pulse flows are beneficial in attracting fish 

and promoting upstream movement. Similar flows will 

occur each year as directed by the NMFS OCAP BO.

Water temperature targets were partially met. The 

60°F target from June 1 through September 15 was 

achieved 77% of the time due to necessary instream 

dredging required for a one-time removal of toxic 

waste from the Spring Creek arm of Keswick Reservoir. 

All of the exceedances occurred during the 56°F 

spawning and incubation period when the target was 

met only 26% of the time.

In 2011, 2 Instream Flow Incremental Methodolo

(IFIM) reports were finalized after peer review

Work continued on bio-validation of the models. 

The resulting 14 IFIM flow-habitat models will b

synthesized with population, temperature, and 

restoration information in 2012 to provide flow 

prescriptions that optimize habitat needs for all 

species, runs and life stages of salmonids in the 

different reaches of Clear Creek, throughout the year.

Instream Flows - Environmental Water Program – 

In FY 2011, CCRP entered into contracts to further the

Environmental Water Program which aims to identify 

and discuss data gaps and uncertainties, understand 

operational tools, identify resources needed, ensure 

safety-of-dams considerations, and mitigate for 

foregone power revenues. Preparations were made 

for an October 2011 workshop to facilitate this 

Program.

Adaptive Management and Monitoring – In 2011,

topographic surveys quantified the amount of fine 

sediment delivered to Clear Creek via a sub-watershed 

that experienced a substantial wildfire in 2008. 

Results indicated that sediment removal, erosion 

inventory and erosion control should be done in future 

years. Additionally, spawning studies for channel 

restoration phases 3A and 3B took place, showing that 

the amount of spawning habitat was greatly increased 

in both phase 3A and 3B, but juvenile rearing habitat 

in phase 3B may need improvements in the future. 

In 2010, the fall-run Chinook escapement was 7,192,

over double of the 3,228 fall-run Chinook observed 

on in 2009. These numbers indicate that despite a 

Central Valley-wide collapse of the fishery, the CCRP is 

continuing to sustain fall-run Chinook populations. 
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

In a free-flowing river, rocks, gravel, dirt and other

substrates are continually moving downstream, 

providing suitable habitat for successful spawning and 

juvenile rearing. The construction of CVP dams has 

had a dramatic impact on streams, by impeding this 

natural process. 

The (b)(13) program represents a continuous effort to 

restore spawning and rearing habitat in three Central 

Valley streams:

•	Upper Sacramento River, from Keswick Dam to 

the Red Bluff Diversion Dam

•	American River downstream of Nimbus Dam 

•	Stanislaus River downstream of Goodwin Dam

The Spawning and Rearing Habitat Program (SRHP) 

focuses on sites that are thought to have the most 

benefit to increase the quality and quantity of 

spawning and rearing habitat. Two criteria guide 

the identification of gravel placement sites: the need 

for spawning habitat; and accessibility to the river by 

truck, helicopter or sluice to deliver the gravel.

Aerial photos, redd (fish egg “nests”) surveys, snorkel 

surveys and boat surveys are used to identify areas for 

gravel augmentation. Prior to placing gravel, baseline 

data is collected using aerial photos, spawning surveys 

and rearing surveys. Once the gravel is placed, the 

SRHP monitors the spawning and rearing occurring at 

and near the restored sites to determine the program’s 

effectiveness. 

The SRHP relies on other river-wide monitoring to 

evaluate population level effects. This consists of adult 

escapement surveys conducted by the Department 

of Fish and Game in the Sacramento, American 

(Reclamation funded), and Stanislaus (Reclamation 

funded) rivers; juvenile production monitoring 

conducted by the Service in the Sacramento River 

(Reclamation funded), and private contractor in 

the Stanislaus River (CVPIA funded). No juvenile

production monitoring is currently occurring in the 

American River. Adult escapement and juvenile 

production monitoring provides information on the 

number of juvenile emigrants produced per spawner.

PERFORMANCE MEASURES

The SRHP places gravel in the Sacramento, Stanislaus 

and American rivers on an annual basis to improve 

spawning and rearing habitat. The annual program 

targets are 10,000 tons on the Sacramento River, 

3,000 tons on the Stanislaus River, and 7,000 tons on 

the American River. 

The program also monitors the effectiveness of gravel 

placement by surveying for several indicators. The 

number of redds per square meter indicates whether 

salmon find the gravel appropriate for spawning (0.03 

redds/square meter is a standard guideline). The 

level of egg retention in females indicates whether 

there are a sufficient number of suitable sites to spawn 

Spawning and Rearing Habitat 

Restoration Program

 3406 (b)(13)

Gravel injection in the Sacramento River just below Keswick 

Dam.
SPAWNING AND REARING HABITAT RESTORATION PROGRAM 3406 (b)(  

FISHERIES

(less than 10% retention is a standard guideline). The 

percentage of salmon using emplaced gravel indicates 

whether the program is providing habitat that is 

suitable (the program aims for 10% on the Stanislaus 

River and 25% on the Sacramento and American 

rivers).

FY 2011 ACCOMPLISHMENTS 

In FY 2011, the SRHP obligated $899,951 from the

Restoration Fund.

Sacramento River – In 2011, the program placed

5,000 tons of gravel just below Keswick Dam, or 50% 

of the annual target of 10,000 tons. Within the gravel 

placement reach, monitoring showed a 6% winter run 

Chinook salmon spawning rate. 

Stanislaus River – In 2011, the program placed

5,000 tons of gravel in Goodwin Canyon. Monitoring 

studies indicate that approximately 21% of spawning 

Chinook salmon used gravel placed by the program. 

American River – In 2011, the SRHP placed 20,770

tons of gravel at upper Sunrise Park, 297% of the 

annual target of 7,000 tons. This included 10,340 

tons of spawning sized material and 10,430 tons 

of oversized material used for side channel habitat 

restoration. Overall, the results indicate that there 

were plenty of gravel sites to choose from in FY 2011, 

allowing for a lower density of redds on any one site. 

The density was measured at 0.01 redd per square 

meter of emplaced gravel. The program monitoring 

data indicates that there was 4% Chinook salmon egg 

retention—well within the 10% goal—indicating that 

females were able to find suitable sites for spawning. 

Riverwide, 51% of steelhead and 47% of Chinook 

spawned on gravel placement projects. The American 

River project was funded by both b13 and AFRP.

Additional monitoring, using a before-after controlimpact framework was conducted to evaluate the 

effectiveness of the projects including: hyporheic 

water chemistry, flow and temperature; gravel 

movement and river bed changes; Chinook and 

steelhead spawning habitat use; juvenile salmonid 

habitat preferences; macro invertebrate production; 

and floodplain inundation. Two years of gravel 

Filling the incised main channel to rewater a dry side channel 

(providing spawning and rearing habitat) at upper sunrise on 

American River.

Front end loaders placing spawning gravel in the American 

River at Upper Sunrise.

Before (top) and after (bottom) gravel placement in the 

American River at upper Sunrise. Note the rewatered side 

channel and gravel placement area.
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

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Sacramento River 

10,000 Ton Target

%

Target

Stanislaus 

River

3,000 Ton 

Target

%

Target

American River

7,000 Ton 

Target

%

Target

1997 22,191 221 2,000 67 0 N/A

1998 22,191 221 3,000 100 0 N/A

1999 15,341 153 0 N/A 6,000 86

2000 29,850 298 1,300 43 0 N/A

2001 0 0 500 17 0 N/A

2002 15,341 153 4,000 133 0 N/A

2003 15,341 153 0 N/A 0 N/A

2004 22,191 221 1,200 40 0 N/A

2005 7,200 72 2,500 83 0 N/A

2006 6,000 60 2,500 83 0 N/A

2007 4,615 46 4,100 137 0 N/A

2008 8,300 83 0 N/A 7,000 100

2009 9,900 99 0 N/A 10,600 151

2010 5,500 55 0 N/A 16,000 229

2011 5,000 50 5,000 167 20,770 297

TOTAL 186,000 126 26,100 58 60,370 57 

Table 14: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2011

Installing woody material to provide juvenile habitat in the 

American River at upper Sunrise.

Front end loader placing spawning gravel in the Stanislaus 

River just below Goodwin Dam.

placements are estimated to have increased floodplain 

inundation by 4.6 acres at 5,000cfs, supporting an 

additional 22,081-237,765 juvenile salmonids (see 

Table 14 for gravel to date summaries).
COMPREHENSIVE ASSESSMENT AND MONITORING PROGRAM 3406 (b)(1  

FISHERIES

modifications, habitat restoration, and fish screens) 

toward meeting AFRP fish production targets. 

Objective #3 – Implement a data management

program to manage CVPIA data (a resource available

to all interested parties), provide training in data 

management, ensure compliance with relevant federal 

laws and regulations, and ensure the effective and 

economical management of resources. 

PERFORMANCE MEASURES

The CAMP Implementation Plan identifies 82

monitoring programs that are required to assess 

progress toward the AFRP fish doubling goals. An 

additional 18 other monitoring programs have been 

identified that relate to AFRP fish production. Of these 

programs, 57 IP programs and all 18 other monitoring

programs relate to Objective #1; and 23 IP programs

relate to Objective #2. 

The 3 Objectives relate to the CAMP goals of 

producing an annual report based on an assessment 

of biological results and effectiveness actions 

(Objectives #1 and #2) and managing CVPIA data,

which include the consolidation, standardization, and 

enhancement of CVP ecosystem data (Objective #3).

FY 2011 ACCOMPLISHMENTS 

In FY 2011, the program obligated $1.7 million from

the Restoration Fund.

Objectives #1

Annual Report — In FY 2011 CAMP produced an

annual report based on 57 of the 82 monitoring 

elements. This report synthesized the data gathered 

under those 57 monitoring elements and assessed 

Pursuant to CVPIA section 3406 (b)(16), the

Comprehensive Assessment and Monitoring Program 

(CAMP) was established to assess the biological 

results and effectiveness of actions implemented by 

CVPIA in support of the fish doubling goal. To meet

this mandate, CAMP produces annual reports that 

compile and synthesize anadromous fish production 

data from the Central Valley. These data are used to 

assess the effectiveness of habitat restoration actions 

such as water management modifications, structural 

modifications, habitat restoration, and fish screens. 

The 2011 CAMP Annual Report reports on 22 Central 

Valley watersheds, and also reports on a broader 

area that includes San Pablo Bay, Suisun Bay, and the 

Sacramento-San Joaquin River Delta.

The program is heavily dependent on other programs 

and agencies to provide information. To optimize its 

program budget, CAMP works with partners whenever 

possible to complete high-priority monitoring projects. 

The CAMP Implementation Plan (IP) was develope

in 1997, and describes methods and procedures for 

monitoring anadromous fish species in California’s 

Central Valley, and for assessing the biological results 

and effectiveness of different categories of restoration 

activities. The plan is based on nine anadromous 

fish taxa: Chinook salmon (fall-, late fall-, winter- and 

spring-run), steelhead, striped bass, American shad, 

white sturgeon and green sturgeon. 

CAMP focuses on three program objectives: 

Objective #1 – Assess the overall effectiveness 

of actions implemented pursuant to CVPIA section

3406(b) in meeting AFRP fish production targets.

Objective #2 – Assess the relative effectiveness 

of categories of CVPIA section 3406 (b) actions

(e.g., water management modifications, structural 

Comprehensive Assessment 

and Monitoring Program

 3406 (b)(16)
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

the cumulative and relative effectiveness of actions 

pursuant to 3406(b) in meeting the AFRP fish 

production targets. 

Acquire New Adult Salmon Data — Two of the 82 

programs relate to the acquisition of new adult salmon 

data. The first is the quantification of the escapement 

of fall-run Chinook salmon on Cow and Cottonwood 

Creeks using weirs with video cameras. The data from 

the cameras was used to determine if the AFRP fish 

production targets on those watersheds were met in 

2011.

The second program relates to the marking and 

tagging of juvenile Chinook salmon at the Coleman 

National Fish Hatchery and the Nimbus Fish Hatchery. 

The marking and tagging of the juvenile salmon 

facilitates the ability to quantify the relative proportion 

of hatchery- vs. naturally-produced adult salmon 

as they return to their natal streams to spawn, and 

thereby increases the accuracy of watershed-specific 

natural production estimates for different salmon 

runs and watersheds in the Central Valley. In 2011,

CAMP marked and tagged juvenile salmon at the 2 

hatcheries, and those activities pertain to 2 of the 57 

activities involving objective #1 and the original 82 

CAMP elements.

Objective #2

Continued the development of a database and 

programming code necessary to generate statistically 

robust, consistently generated juvenile Chinook 

salmon production estimates and confidence intervals 

from across the Central Valley. The juvenile salmon 

production estimates will provide a basis for assessing 

the biological response to habitat restoration projects 

in multiple watersheds. The data will also provide 

basic information pertaining to juvenile salmon 

demography, outmigration timing, and ecology.

Monitored the production of juvenile Chinook salmon 

that are produced by the Stanislaus River, with the 

goal of using that data to assess the effectiveness of 

habitat restoration activities in that watershed.

Continued to obtain support from Instream Flow

Incremental Methodology (IFIM) staff to evaluate t

relationship between river discharge levels and the 

acreage of floodplain inundated on the Stanislaus 

River. The data will be used in conjunction with 

juvenile salmon production data to assess the effects of 

floodplain restoration activities along the banks of the 

Stanislaus River.

Objective #3 

Data Management Plan — The program is 

currently developing a CVPIA data acquisition

and management plan (DAMP). Additionally, a 

contract has been entered to determine the most 

efficient methods of creating and implementing an 

accomplishments database. 

Develop Metadata Tools — The program developed 

a GIS tool to provide easily obtained geographic

information on streams, dams, and other geofeatures related to CVPIA projects. The program also

developed an Excel spreadsheet that allows users to 

enter metadata related to their projects. Funds have 

been allocated to expand previous work so that a 

web-based GIS portal will be created. This portal will

allow users to access CVPIA documents using GI

Other Data Management — Metadata files were 

created for a number of data sets and documents. 

These included data for Fisheries (Chinookprod) and 

Refuges (Water Delivery data).
ANADROMOUS FISH SCREEN PROGRAM 3406 (b)(21) 5

FISHERIES

The Anadromous Fish Screen Program (AFSP) works 

together with the State of California to construct, 

replace and rehabilitate fish screens, and relocate 

diversions throughout the Central Valley and 

Sacramento-San Joaquin Delta. The AFSP strives to 

improve the effectiveness and efficiency of fish screens, 

and collaborates with other agencies to encourage the 

dissemination of information. The program also seeks 

to reduce the overall cost of fish screens. These efforts 

support the fish doubling goal by protecting juvenile 

Chinook salmon, steelhead, green sturgeon and white 

sturgeon from entrainment and predation at priority 

water diversions. 

The AFSP provides matching funds for state and 

local funding, providing up to 50% of the cost of a 

fish screen project. The AFSP conducts monitoring 

at diversions and many fish screens to determine the 

critical factors related to fish losses, and to assure the 

effectiveness of constructed fish screens. Fish screen 

projects are complex, and are typically constructed 

in phases over several years. The four key project 

phases include a feasibility study, preliminary design, 

final design, and construction. Once a screen is 

constructed, the diverter is solely responsible for its 

ongoing operation and maintenance.

PERFORMANCE MEASURES

The AFSP’s key performance measure is to assist the 

State of California in developing and implementing 

measures to avoid juvenile anadromous fish losses 

resulting from unscreened or inadequately screened 

diversions. This is accomplished primarily by 

installation of fish screens. Progress is measured in 

the number of fish screens constructed, with a target 

of screening the priority unscreened diversions on 

prescribed watersheds. The AFSP and the State of 

California are currently conducting fish entrainment 

monitoring at representative unscreened diversions 

to evaluate potential fish screening benefits and to 

determine the highest priority diversions for screening.

FY 2011 ACCOMPLISHMENTS 

The AFSP obligated funding from the Restoration Fund 

in the amount of $3.9 million, $349,200 from Water 

and Related Resources Fund, and $2.0 million from 

Bay-Delta Fund. 

Screening Diversions –Construction continued on 

of the American Basin (Natomas Mutual) Fish Screen 

Project (Phase I) for a screened diversion at Sankey

on the Sacramento River that replaces two existing 

diversions on the Natomas Cross Canal. This project 

also results in the removal of an anadromous fish 

migration barrier (seasonal diversion dam) on the 

Natomas Cross Canal. This fish screen project will be 

completed in FY 2013.

The AFSP continued to support design, environmental 

compliance, and permitting activities for the 

Reclamation District 2035 Fish Screen project on the 

Sacramento River. This fish screen project is expected 

to begin construction in FY 2013.

The AFSP completed construction of the Patterson Fish 

Screen, consisting of a 195 cfs capacity vertical flat 

plate fish screen on the San Joaquin River. This fish 

screen protects outmigrating Chinook salmon and 

steelhead as well as resident game and non-game fish 

from entrainment. 

Three cylindrical fish screens were constructed: Sutter 

Mutual Portuguese Bend (106 cfs), Oji Brothers 

Farms (28 cfs) and Windswept Land & Livestock #3 

(9 cfs). The monitoring program associated with 

Anadromous Fish Screen 

Program

 3406 (b)(21)
52 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

potential lower cost options for minimizing fish losses 

at smaller diversions, such as use of behavioral devices 

at some diversions rather than use of more expensive 

positive barrier screens. A final study report will be 

issued in FY 2013.

these screens is conducted in partnership with the 

Family Water Alliance. The program collects data to 

assess the biological benefits of fish screening and 

to help prioritize future fish screening efforts. The 

2011 activities included fish entrainment monitoring at 

nine diversion sites, in addition to screening the three 

diversion sites.

The AFSP continued to support design, environmental 

compliance and permitting activities for the City of 

Yuba City Fish Screen project for a 74 cfs diversion on 

the Feather River. This fish screen project is expected 

to begin construction in FY 2012 (see Table 15 for 

projects by watershed).

AFSP Technical Assistance – The AFSP continued a 

two-year (2010-2011) hydraulics and fish behavioral 

study at the UC Davis J. Amorocho Hydraulics 

Laboratory to identify critical factors resulting in fish 

losses at water diversions. The study will identify 

Table 15: AFSP Projects by Watershed 

and Cubic Feet per Second (cfs) 

Screened, 1994-2011

Watershed

Number of

 Fish Screens

Flow

(cfs)

Sacramento 19 3,954

American 1 210

Yuba 1 65

Butte 4 257

Delta 6 113

San Joaquin 2 455

TOTAL 33 5,054

Aerial view of the Patterson Fish Screen
SAN JOAQUIN RIVER RESTORATION PROGRAM 3406 (c)(  

FISHERIES

PERFORMANCE MEASURES

The Settlement includes two goals:

Water Management – To reduce or avoid adverse 

water supply impacts to all of the Friant Division longterm contractors that may result from implementation of 

the Settlement. (The Settlement calls for interim flows 

and restoration flows, which are additional releases 

out of Friant Dam to support fish and wildlife habitat 

needs.) 

Restoration – To restore and maintain fish 

populations in “good condition” in the mainstem 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.

FY 2011 ACCOMPLISHMENTS 

The Program obligated $717,821 from the CVPIA

Restoration Fund to achieve the following:

Invasive Vegetation Management and Control – 

In support of the Restoration Goal, Reclamation

identified the need to manage and control invasive 

vegetation as part of the environmental compliance 

and permitting activities for the Water Year 2011 

and 2012 Interim Flows, and specifically as part of

Reclamation’s Water Year 2011 and 2012 Interim

Flows Environmental Assessments (EAs). The Invasive

Vegetation Management Plan calls for monitoring and 

control and management activities focusing on five 

species, red sesbania, salt cedar, giant reed, Chinese 

tallow, and sponge plant. These activities will begin in 

FY 2012. 

The San Joaquin River is a major tributary to the 

Sacramento-San Joaquin Delta, historically providing 

flows from the southern Central Valley. Section 

3406(c)(1) mandates the preparation of a reasonable, 

prudent and feasible comprehensive plan to 

reestablish and sustain naturally reproducing salmon 

in the San Joaquin River below Friant Dam to the 

confluence with the Sacramento-San Joaquin Delta 

Estuary. 

Subsequent to the passage of CVPIA, a Stipulation

of Settlement (Settlement) was reached in September 

2006 that resolved long-standing disputes related 

to Reclamation’s operation of Friant Dam. The 

Settlement ended an 18-year lawsuit between the 

U.S. Departments of the Interior and Commerce, the

Natural Resources Defense Council (NRDC) and the 

Friant Water Users Authority (FWUA). 

Public Law 111-11 authorizes and directs the Secretary 

of the Interior to fully implement the Settlement and

to use the CVPIA 3406(c)(1) to fund and implement

a portion of the program. Public Law 111-11 also 

specifies that “...the Settlement satisfies and discharges 

all of the obligations of the Secretary contained 

in section 3406(c)(1)...” The San Joaquin River 

Restoration Program (SJRRP) implements the Settlement 

consistent with Public Law 111-11.

The agencies responsible for the management of 

the SJRRP include Reclamation (lead), the Service, 

National Marine Fisheries Service (NMFS), California 

Department of Water Resources (DWR), and 

California Department of Fish and Game (CDFG). 

Please refer to the SJRRP website for a complete status 

of all actions: www.restoresjr.net.

San Joaquin River Restoration 

Program

 3406 (c)(1)
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

Annual Technical Report and Annual Monitoring 

and Analysis Plan – In support of the Restoration

Goal, the SJRRP’s Implementing Agencies have

developed and are implementing an annual cycle of 

identifying study needs and monitoring activities and 

providing for timely release of all quality controlled 

monitoring data. In FY 2011, the SJRRP produced the

Final 2011 Monitoring and Analysis Plan (Agency 

Plan) in November 2010; the 2010 Annual Technical 

Report in April 2011, and the 2012 Monitoring and 

Analysis Plan in November 2011. 

In FY 2011, Reclamation also funded the Annual

Technical Report and Monitoring and Analysis Plan 

efforts. This effort also includes coordination of 

the SJRRP’s Restoration Goal Technical Feedback 

Group meetings that facilitates the timely release and 

discussion of monitoring data, upcoming monitoring 

efforts, and provides for early input in the Program’s 

high priority construction projects. Activities under the 

contract will begin in FY 2012. 

Fish Population Modeling – In FY 2011 and

in support of the Restoration Goal, Reclamation 

also issued a contract for the development of a 

fisheries population model to support the continued 

development of the SJRRP Fisheries Management 

Plan and selection of alternative actions including the 

release and routing of flows, salmon reintroduction, 

and the construction of site-specific projects. The 

modeling effort will utilize the Ecosystems Diagnosis 

and Treatment modeling platform and “proof of 

concept” model previously prepared for the San 

Joaquin River. The effort will apply the Ecosystems 

Diagnosis and Treatment model to addressing fish 

management questions and site-specific planning and 

evaluation needs as well as improve the model. These 

efforts will begin in FY 2012. 

The above accomplishments were achieved with 

CVPIA funding. To see all SJRRP accomplishments,

visit www.restoresjr.net. 

Don Portz, with Denver’s TSC, talks with Fresno Bee reporter 

Mark Grossi about the study.
SAN JOAQUIN RIVER RESTORATION PROGRAM 3406 (c)(  

FISHERIES

Norm Ponferrada with Denver’s Technical Service Center, listens for acoustically tagged fist movement at the Hills Ferry Barrier 

on the San Joaquin River. The barrier is seasonally installed by the California Department of Fish and Game to prevent fallrun Chinook salmon from migrating upstream in the SJR from the Merced River. This study led by the TSC is evaluating the 

effectiveness of the barrier – one of many studies funded by the CVPIA to support the SJRRP’s Monitoring and Analysis Plan.
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

FISHERIES

low-lift pumps would help meet salinity objectives for 

the southern Delta standards.

The Clear Creek inSALMO application was completed 

in FY 2011. The application provides opportunities to 

study how proposed habitat restoration actions might 

affect the spawning, rearing and emigrating juvenile 

production of salmon on restoration sites at Clear 

Creek. Reclamation and the U.S. Fish and Wildlife 

Service (Service) continuously seek opportunities 

to work with the National Marine Fisheries Service 

(NMFS) and other Federal and State fishery agencies 

to develop other salmon life-cycle models to meet 

biological and restoration modeling needs. 

In FY 2011, the Service completed the Sacramento

River Water Quality Model (SRWQM) extension 

from Knights Landing to Freeport, California. This 

temperature model extension provided opportunities 

for further expansion of the SRWQM to incorporate 

the Feather and American Rivers. 

The water management model (CalLite 2.0) and 

the Graphical Users’ Interface (GUI) were bein

developed in 2011. CalLite is an optimization and 

screening model that can simulate the hydrology, 

reservoir and project operations, and salinity 

responses. In FY 2011, the GoldSim (a proprietary

Monte Carlo Simulation software) codes were 

replaced by flexible (developed in-house) Water 

Resources Simulation Language codes. Water 

Resources Integrated Modeling System was used to

compile the codes. An interactive CalLite Graphical 

User Interface GUI was developed to setup a

interactive CalLite GUI alternatives, run executables,

and to analyze results. The User’s Documentation, the 

Developer’s Reference, the design and the Technical 

Specifications, the funding for the GUI development

The goal of the Ecosystem and Water Systems 

Operations Models Program is to develop broadly 

available and readily usable models and supporting 

data to evaluate the ecologic and hydrologic effects 

of existing and alternative operations of public and 

private water facilities and systems in the Sacramento, 

San Joaquin, and Trinity River watersheds. The 

primary purpose of this effort is to support the 

Secretary’s efforts in fulfilling the requirements of 

CVPIA through improved scientific understanding

As part of the model development process, the 

Program continues to support hydrologic, physical 

and biologic model development, and data collection 

activities. 

PERFORMANCE MEASURES

Develop Models - Develop readily usable and broadly 

available models and supporting data to evaluate 

existing and alternative water management strategies. 

Section 3406 (g) of the CVPIA anticipates that Interio

will develop data and/or models to improved scientific 

understanding in nine integral areas. 

FY 2011 ACCOMPLISHMENTS 

The Modeling Program obligated $800,800 from the 

Restoration Fund in 2011. 

The DSM2 model is being used for various purposes 

in CVPIA, but has had limited contributions from the

3406 (g) program. In FY 2011, the DSM2 model was

modified and applied to investigate the installation 

of low-lift pump operations and alternatives at the 

Old River temporary barriers. The DSM2 modeling 

objective was to determine if the operation of these 

Ecosystem and Water Systems 

Operations Models

 3406 (g)
ECOSYSTEM AND WATER SYSTEMS OPERATIONS MODELS 3406 (g) 5

FISHERIES

Table 16: Ecosystem and Water System Operations Models That are Developed by 3406(g)

 Program

Model Type Models Developed To Date FY 2011 Accomplishments

Comprehensive water budget 

of surface and groundwater 

supplies 

CalSim II, CalSim 3.0 CalLite, HGS, 

ECOSIM-W and DSM2

The results of the HGS- CalSim linkage and 

pilot application were presented at the 2011 

annual meeting of the California Water and 

Environmental Modeling Forum (CWEMF). 

After reviewing the contractor’s progress for 

scheduling and budget, Reclamation decided 

not to pursue additional model development. 

Related water quality 

conditions, including 

temperature dynamics related 

to storage

Upper Sacramento River Water Quality 

Model (SRWQM). San Joaquin Basin 

Temperature Model

SRWQM model was extended from Knights 

Landing to Freeport.

Surface-ground and streamwetland interactionsHydroGeoSphere, CVHGSM (Central 

Valley HydroGeoSphere Model)

Reclamation collaborated with USGS to retrieve 

data from the USGS Central Valley Database to 

generate information as inputs for use with the 

HGS Central Valley application development.

Ecosystem modeling - flow 

needs to meet restored 

carrying capacity of streams

inSALMO inSALMO Clear Creek application was 

completed in September 2011. 

Ecosystem modeling - flow 

to store and maintain natural 

channel and riparian habitat 

values

RHEM No new work was done in 2011 for the model.

Water operations models - 

CVP and SWP operations

CalSim II, CalSim 3.0 CalLite and 

ECOSIM-W

Several improvements were made to Calsim 

II, like improved representation of baseline 

conditions, Isolated Facility, CVP/SWP sharing 

of export restrictions under the D-1641 exportinflow ratio, and releases to meet the D-1641 

salinity standards in the Delta in conjunction 

with exports CalSim 3.0 is scheduled for public 

release in FY 2012. CalLite 2.0 (Sacramento 

Basin application) and the GUI are scheduled 

for publicly release in FY 2012.

Ecosystem modeling in 

support of sustainable fish 

harvest levels, including 

tradable harvest rights 

This currently has none of the limited available 

resources being dedicated to it. This is 

currently not a high priority for the program.

Ecosystem modeling to 

identify opportunities to 

protect and restore wetland 

and upland habitat

inSALMO Completed inSALMO Clear Creek application 

development. Reclamation and Service will 

coordinate with NMFS to seek opportunity for 

another ecosystem model development.

Water management modeling 

to include firm CVP yield

CalSim II, CalSim 3.0, CalLite and 

ECOSIM-W

CalLite model was used to develop an 

application for the Central Valley Project 

Integrated Resources Plan (CVPIRP) 

application in FY 2011.

and that for the XA Solver license, the training etc. 

were provided by the 3406(g) fund. The model is 

planned to be available in FY2012.

In FY 2011, Reclamation and the U.S. Geological

Survey (USGS) staff reviewed the existing USGS 

Central Valley Data Base and GIS data to retrieve

data/information. This information will subsequently 

be used as input for the HydroGeoSphere Central 

Valley Model (CVHGMS) application.

The 3406 (g) program also prepared publications 

and provided support to model applications for 

stakeholders. Table 16 presents the nine model types 

and FY11 accomplishments.

All of the projects that were undertaken in FY2011 met 

or exceeded the performance targets.

Central Valley Project Improvemen

Chapter 3

CVP WATER 

OPERATIONS

RESOURCE 

AREA
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

WATER OPS

An adequate flow of water in rivers and streams 

is essential for all stages of fish life: spawning, fry 

emergence, juvenile development, outmigration 

and passage back to spawning grounds. Flows 

help maintain a healthy environment for fisheries 

by maintaining sufficient stream depth and optimal 

temperatures for spawning and rearing. Periods 

of high flow also move sediments downstream to 

establish and maintain the river bottom. Reclamation 

and the Service are dedicated to creating optimal 

flows to support the goal of doubling the population of 

anadromous fish. 

Determining the instream flow needs in CVP streams 

is an ongoing process that is being addressed by 

Instream Flow Incremental Methodology (IFI).  T

habitat-based model was developed by the Service 

to assess instream flow needs for aquatic resources, 

including anadromous fish. 

IFIM studies involve four basic steps: 1) monitoring 

stream to assess current conditions, 2) modeling to 

determine optimal flows for current conditions, 3) peer 

review of modeling results to ensure accuracy, and 4) 

preparation of a final report to document findings. 

IFIM studies funded under section (b)(1)(B) focuse

solely on CVP streams: American, Sacramento, and 

Stanislaus rivers and Clear Creek. The program goal 

was to complete up to nine IFIM studies to infor

modification of CVP facilities in order to improve 

instream conditions for all life stages of anadromous 

fish. The program completed the ninth IFIM study i

2007.

The information developed by the IFIM is use

by (b)(2) program managers in developing 

recommendations for modifying instream flows in CVP 

streams to reduce redd (fish egg “nests”) dewatering, 

reduce juvenile stranding and provide suitable 

instream conditions. This involves changing and 

coordinating planned releases between CVP dams 

when such releases will improve instream conditions 

without affecting other CVP obligations or authorized 

purposes.

PERFORMANCE MEASURES

Modify Operations – The IFIM studies will infor

how to vary CVP flows modifications depending on 

hydrology and biological conditions. 

FY 2011 ACCOMPLISHMENTS 

No funds were obligated from the Restoration Fund in 

FY 2011 for the MOP. 

Modify Operations

The data generated by IFIM studies have been use

by the Service and Reclamation to modify operations 

on CVP streams.

Clear Creek: Operations were modified on Clear 

Creek throughout the year to augment low base 

flows and provide spring attraction flows to improve 

conditions for fall-run Chinook salmon, spring-run 

Chinook salmon, and steelhead during spawning, 

incubation, and rearing. 

Sacramento: Operations were modified on the 

Sacramento River in February to maintain a flow 

rate of approximately 3800-4000 cfs to improve 

conditions for late fall- and fall-run Chinook salmon 

spawning and emergence.

Modified CVP Operations

 3406 (b)(1)(B)
FLOW FLUCTUATIONS AND RESERVOIR STORAGE 3406 (b)(9) & (19  

WATER OPS

Carryover Storage – Maintain 1,900,000 acre-feet 

(AF) of carryover storage levels at Shasta Reservoir 

and 600,000 AF at Trinity River Reservoir. 

FY 2011 ACCOMPLISHMENTS 

The FFP obligated $35,691 from the Restoration Fund 

in FY 2011. 

Flow Fluctuation

Clear Creek, American River, and Sacramento 

River – As part of an investigation funded by the 

3406 (b)(2) Dedicated Yield Program, biologists 

surveyed salmon and steelhead redds in fall and 

winter of 2010-2011 on the American River. Insights

gained will help make informed decisions pertaining 

to flow fluctuations as well as the potential use of (b)(2) 

dedicated yield.

American River – The American River Operations 

Work Group commissioned one salmonid isolation 

pool survey (August 2011) and multiple steelhead 

redd surveys (December 2010 – April 2011). In the

isolation pool survey, no stranded juveniles were 

observed. The steelhead redd surveys in conjunction 

with visual counts are being used to monitor trends in 

in-river spawning steelhead abundance in the lower 

American River.

Stanislaus River – The Stanislaus Operations 

Group held monthly meetings to discuss and provide 

recommendations for achieving the minimum instream 

flow requirements and temperature objectives 

contained in the BO. The Stanislaus Flow Fluctuation 

Study was completed by CDFG. The group also 

River and stream flow fluctuations can result in fish 

losses through mortality of migrating and spawning 

adults, decreased egg viability in redds due to 

thermal distress, redd dewatering and isolation, and 

stranding of juveniles. The goal of the (b)(9) Flow 

Fluctuation Program (FFP) is to minimize these losses by 

moderating changes in CVP releases on Clear Creek 

and the Sacramento, American, and Stanislaus rivers. 

The (b)(19) Reservoir Storage Program (RSP) seeks 

to maintain carryover water storage at Shasta and 

Trinity reservoirs and deliver appropriately timed flows 

and flows of adequate quality to support fisheries 

restoration and meet other project purposes. 

In order to manage the program and reasonable and

prudent alternatives (RPAs) contained in the 2009 

NMFS OCAP BO, they program engages in sets of 

actions that vary based upon Shasta Reservoir endof-September storage. These sets of actions broadly 

relate to the flow release schedule for Keswick Dam 

and Trinity Dam to maintain cold water supplies 

necessary for egg incubation for the following 

summer’s cohort of winter-run. Depending on the 

water year type and amount of carryover storage 

at the end of September, the BO mandates close 

coordination between NMFS, California Department 

of Fish and Game (CDFG) and the Service to schedule 

releases for the subsequent year.

PERFORMANCE MEASURES

Flow Fluctuation – Eliminate, to the extent possible, 

fish losses on CVP streams due to flow fluctuations 

caused by operation of CVP facilities. 

Flow Fluctuations and Reservoir 

Storage

 3406 (b)(9) & (19)
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

WATER OPS

Table 17: Carryover Storage at Shasta and Trinity Reservoirs, 1998-2011

Water 

Year

Sac. Valley Index 

Water Year Type

Shasta Reservoir 

(Storage Target = 1.9 MAF*)

Trinity Reservoir 

(Storage Target = 600 TAF)**

1998 Wet 3.4 MAF 2,077 TAF

1999 Wet 3.3 MAF 1,962 TAF

2000 Above Normal 3.0 MAF 1,791 TAF

2001 Dry 2.2 MAF 1,428 TAF

2002 Dry 2.6 MAF 1,500 TAF

2003 Above Normal 3.2 MAF 1,881 TAF

2004 Below Normal 2.2 MAF 1,591 TAF

2005 Above Normal 3.0 MAF 1,890 TAF

2006 Wet 3.2 MAF 1,795 TAF

2007 Dry 1.9 MAF 1,461 TAF

2008 Critical 1.4 MAF 1,137 TAF

2009 Dry 1.8 MAF 919 TAF

2010 Below Normal 3.3 MAF 1,558 TAF

2011 Wet 3.3 MAF 2,167 TAF

* million acre-feet

** thousand acre-feet

helped coordinate fish monitoring studies and habitat 

mapping. 

Carryover Storage

The RSP met the carryover targets for Shasta and 

Trinity reservoirs in FY 2011 (see Table 17). Due to 

high precipitation and inflow to the reservoirs, the 

RSP met the carryover targets for Shasta and Trinity 

reservoirs in FY 2011. This helps to ensure that the 

next water year starts with a good base supply and a 

large cold water pool to meet the various temperature 

requirements on the rivers for the fish species.
Central Valley Project Improvemen

Chapter 4

REFUGES

RESOURCE 

AREA
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

The Refuge Water Supply Program (RWSP) is 

comprised of three components: 

3406 (b)(3) Refuge Water Acquisition – Acquisition 

of Incremental Level 4 quantities specified in 3406 (d

(2).

3406 (d)(1), (2) & (5) Refuge Water Conveyance – 

Delivery of Level 2 water and Incremental Level 4

water, and construction of water delivery facilities.

3406 (d)(5) Refuge Facilities Construction 

Actions – Infrastructure construction to provide full

Level 4 water supplies to the boundary of the CVPIA

refuges. 

This component supports delivery of water to those 

lands identified in the Report on Refuge Water Supply 

Investigations (March 1989), and the San Joaquin

Basin Action Plan/Kesterson Mitigation Action Plan 

(December 1989).

The RWSP’s goal is to ensure that all CVPIA identified

wetland habitat areas, hereinafter referred to as 

“refuges”, annually receive water of specified quantity, 

of suitable flow rate and timing, and suitable quality 

to support their wetland and aquatic environments. A 

total of 19 refuges are served by the program (shown 

in Figure X). 

The RWSP’s water accounting of acquisitions and 

deliveries is based on Reclamation’s Mid-Pacific 

Region’s water service contract year. The contract 

year begins March 1 and ends on the last day of 

February the following year. The RWSP components—

acquisition, conveyance, and construction—work 

together to implement the goals of CVPIA related to

refuges. 

The RWSP’s two water types are defined as Level 2 

water and Incremental Level 4 water.

•	Level 2 is the amount of water required 

for minimum wetlands and wildlife habitat 

management based on historic average annual 

deliveries before 1989. Reclamation is required 

to provide full Level 2 water supplies annually. 

The Level 2 annual water delivery target is 

422,251 acre-feet (AF), including 26,007 

acre-feet of replacement water. Replacement 

water was originally provided by tailwater and 

groundwater but is now included in Level 2 

water supplies due to water quality concerns. 

•	Incremental Level 4 water is the difference

between Level 2 and Full Level 4 water supplies; 

it equals 133,264 AF.

Full Level 4 is the total annual amount of water 

identified for each refuge in CVPIA as required for

optimum wetlands and wildlife habitat development 

and management. The Full Level 4 water delivery 

target for the 19 refuges is 555,515 AF and is met 

when Level 2 and Incremental Level 4 water targets

are met in full. 

Each year, Reclamation strives to provide as 

much Incremental Level 4 water as possible. The

CVPIA specifies that Reclamation must acquire this

Incremental Level 4 water supply through voluntary

measures such as water conservation, conjunctive use, 

purchase, lease, donation, or similar activities.

LONG-TERM SUPPLY 

CONTRACTS PROVIDE 

STABILITY FOR REFUGE 

OPERATORS

To ensure reliability for refuge managers, Reclamation 

entered into long-term water supply contracts with 

the three refuge managing agencies: California 

Department of Fish and Game (CDFC), the Service, 

Refuge Water Supply Program

 3406 (b)(3), (d)(1), (2) & (5)
REFUGE WATER SUPPLY PROGRAM 3406 (b)(3), (d)(1), (2) & (5) 65

REFUGES

and Grassland Water District (GWD). These contracts 

have a performance period of 25 years and are 

renewable, representing Reclamation’s obligation 

under CVPIA to provide identified quantities of water

to certain refuges in the Central Valley. 

Each year in February and monthly thereafter through 

May, Reclamation’s Central Valley Operations Office 

announces the water supply allocation available 

to the CVP contractors and CVPIA refuges (Level

2 water) for the current contract year. Each year 

between February and March, the RWSP provides 

the Interagency Refuge Water Management Team

(IRWMT) with an initial projection of anticipated

Incremental Level 4 water purchases for that contract

year. The IRWMT determines the allocation of the

projected Incremental Level 4 supplies. The IRWM

is comprised of representatives from Reclamation, the 

Service, CDFG, GWD, and the Central Valley Joint 

Venture. The creation of this team was established 

through a provision in the long-term water supply 

contracts. Concurrent to this process, the three refuge 

managing agencies develop their initial water delivery 

schedules for each refuge by March 1. 

USE OF GROUNDWATER FOR 

REFUGE WATER SUPPLIES

The RWSP strives to diversify its water sources. For 

example, the RWSP pursues groundwater projects 

in partnership with local water districts because 

groundwater does not require external conveyance 

if the source can be located at or near a refuge. The 

lower cost of groundwater is also an advantage, 

although downsides include groundwater of poorer 

quality in some locations, particularly in the San 

Joaquin Valley; threat of aquifer depletion; and land 

subsidence. The RWSP relies on refuge managers 

to monitor groundwater quality for toxins, pollutants 

and salinity so as not to degrade the general quality 

of water on the refuges. To further that effort, in FY 

2011, the RWSP continued funding a Real Time Water 

Quality Monitoring Project to study the salt load 

effluent from refuges in the San Joaquin Valley.

In FY 2011, several refuges relied at least in part on

groundwater supplies, including Volta and Gray Lodge 

Wildlife Areas (WA), Merced and Pixley National 

Wildlife Refuges (NWR) and Grassland Resource 

Conservation District (RCD). Additionally, the RWSP 

completed construction of two new wells at the Volta 

WA in FY 2011 that will increase groundwater supplies 

to both Volta WA and Grasslands RCD. 

REFUGE BENEFITS

Numerous biological benefits have resulted from 

a reliable year-round water supply through CVPIA

that adequately meets the delivery schedule for 

wetland management on CVPIA refuges. Habitat

is now available during the months of August and 

early September that benefits early arriving migrant 

waterfowl and shorebirds; habitat is also provided for 

resident wildlife and their young during the spring and 

summer, when wetland habitat can be particularly 

limited by hydrology. Introducing water for semipermanent and permanent wetland habitat in the

spring and summer directly benefits the recovery of 

special status species such as the giant garter snake, 

and tricolored blackbirds. 

Wintering wildlife also benefit from this habitat 

diversity, as seasonal wetlands are now managed 

to coincide with peak migration times of shorebirds 

and waterfowl. Timely de-watering and irrigations 

promote the germination and irrigation of important 

moist-soil food plants, such as swamp timothy and 

watergrass. These plants provide a high-energy 

food source through both their seeds and associated 

invertebrate communities.
66 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

Figure 7. Central Valley Refuges Receiving CVPIA Water Supplies

Refuge or Wildlife Area

Major Road

City

San Luis National 

Wildlife Refuge Complex

East Bear Creek Unit

Freitas Unit

Kesterson Unit

San Luis Unit

West Bear Creek Unit

North Grasslands 

Wildlife Area

 Salt Slough Unit

 China Island Unit

Merced National

Wildlife Refuge

Los Banos Wildlife Area

Grassland Resource

Conservation District

Volta Wildlife Area

Mendota Wildlife Area

Gray Lodge

Wildlife Area

Sutter National

Wildlife Refuge

Pixley National Wildlife Refuge

Kern National Wildlife Refuge

Sacramento National

Wildlife Refuge

Delevan National

Wildlife Refuge

Colusa National

Wildlife Refuge

CVPIA REFUGES

Sacramento

San Francisco

Los Angeles
WATER ACQUISITION PROGRAM - REFUGE WATER 3406 (b)(3) & (d)(  

REFUGES

The Refuge Water Acquisition Program (RWAP) 

is responsible for the acquisition of133,264 acrefeet (AF) of Incremental Level 4 Water (also called

supplemental water) for critical wetland habitat 

supporting resident and migratory waterfowl, 

threatened and endangered species, and wetland 

dependent aquatic biota on the refuges.

Presently, Incremental Level 4 (Inc L4) water consists o

annual purchases from willing sellers from both surface 

and groundwater supplies. In 1998 and 2005 the

RWAP acquired 9,300 AF of permanent Inc L4 surface

water supplies. The RWAP also acquires a portion of 

water supplies at no cost, including rescheduled water, 

215 water, and water delivered under a mitigation 

agreement with the Federal Energy Regulatory 

Commission. 

The RWAP continues to use groundwater to lower 

costs and increase reliability of providing supplemental 

refuge water supplies with acquisitions from Grassland 

Water District (GWD) and by groundwater wells. The 

groundwater wells will increase water supply reliability 

and help to diversify Level 2 Water. It is anticipated

that these wells will produce up to 5,000 AF annually.

PERFORMANCE MEASURES 

Acquisition - The RWAP’s goal is to acquire enough 

water to deliver 133,264 acre-feet (AF) of Inc L4

water to refuge boundaries annually (i.e. 133,264 

AF plus any additional water needed to cover 

conveyance losses), excluding replacement water.

FY 2011 ACCOMPLISHMENTS 

The RWAP obligated a total of $12,616,343 from 

the Restoration Fund, and $250,000 from the Water 

and Related Resources Fund. Of this, $11,500,000 

was obligated for water acquisitions, $500,000 was 

applied to the Real-time Water Quality Monitoring 

project, $201,000 was applied to the South-of-Delta 

(SOD) coordinator duties, $113,000 was obligated 

towards groundwater assessment, and the remainder 

of funds covered program administration.

The RWAP obligated $8,307,694 for the purchase 

of 81,811 AF of water for Water Year 2011 and 

$3,200,000 was obligated for the future purchase 

of water for Water Year 2012. Additionally, 22,511 

AF for WY 2011 was acquired at no cost through 

various other sources representing the total acquisition 

of 78% of the Inc L4 water delivery target (Table 18).

This water was acquired for delivery in the 2011 water 

year which covers a portion of calendar year 2010 

and a portion of calendar year 2011.

Gadwalls, Kern NWR

Refuge Water Acquisition

 3406 (b)(3) and (d)(2)
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

Table 18: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2011

Fiscal Year*

Incremental Level 4 

Water Acquired (AF)

Percent of Incremental Level 4 

Target (133,264 AF)

2002 85,390 64

2003 70,000 53

2004 67,710 51

2005 70,962 53

2006 83,822 63

2007 41,111 31

2008 30,308 23

2009 31,726 24

2010 62,238 47

 2011** 104,322 78

Average 64,759 49

* This table reflects acquisitions starting with Fiscal Year 2002, the first year that CVPIA mandated Full Level 4 deliveries for all refuges 

 [Section 3046 (d)(2)]. 

** 2011 is the first year the Program is reporting purchased and non-purchased water acquired toward the Incremental Level 4 target. 

The 81,811 AF of purchased water was acquired from 

a variety of surface and ground water sources. An 

additional 18,686 AF of water was acquired without 

cost to Reclamation. Both purchased and no-cost 

supplies brought the Inc L4 water to 104,322 AF,

which includes water to account for conveyance losses 

such as seepage and evaporation. Of the 104,322 

AF, approximately 95,000 AF of full Level 4 water 

was actually delivered to the nine SOD refuges and 

3,000 to Delevan NWR, a North-of-Delta (NOD) 

refuge. See the next section on Conveyance for more 

information on water deliveries. 

The RWAP continued funding to Grassland Water 

District to implement the Real-time Water Quality 

Monitoring Project in the Grasslands Ecological Area 

(GEA), a State-designated geographic area in the San 

Joaquin Valley that encompasses wetlands consisting 

of 12 SOD CVPIA refuges. The study monitors quality

of the water after it is applied to refuges, as this water 

eventually returns back into the surface water system 

and discharges to the lower San Joaquin River. Data 

from the extensive array of water quality monitoring 

stations in this project will provide information to 

refuge and land-use managers that will serve to better 

understand the flow and water quality contributions to 

the lower San Joaquin River, specifically as it relates to 

meeting the California Regional Water Quality Control 

Board’s TMDL standards.

The RWAP co-funded with the Refuge Conveyance 

Program construction of 2 wells at Volta Wildlife Area 

under the American Recovery and Re-investment Act. 

This project was completed in FY 2011. The expected 

production capacity of these wells is approximately 

5,000 acre-feet per year after the first year of 

production. The water will be equally split between 

Level 2 diversification and Inc L4 water supplies.

FY 2011 was the first year since CVPIA was enacted

that full Level 4 water (Level 2 and Inc L4) was made

available to eleven of the 14 SOD wildlife refuges. 

This is significant because these refuges are located 

in a hydrologically dry area and often lack ample 

water to maintain wetland habitat. Due to external 

conveyance infrastructure constraints, two refuges--East 

Bear and Pixley NWRs--were not able to receive full 

Level 4 water. The third refuge that did not receive 

full Level 4 water, Merced NWR, received sufficient 

water supplies from non-CVP sources in FY 2011. For 

refuges NOD, Inc Level 4 water supplies were only

acquired for Delevan NWR. The Sacramento and 

Colusa NWRs employed water conservation measures 

that enabled them to be managed with Level 2 water 

supplies. Insufficient external conveyance facilities

currently preclude delivery of full Level 4 water to 

Gray Lodge WA and Sutter NWR. 
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 69

REFUGES

The Refuge Water Conveyance (Wheeling) Program 

(RWCP) is responsible for providing long-term, firm 

and reliable water deliveries to the 19 Federal, State, 

and private wetlands and wildlife habitat areas 

(collectively referred as refuges) located in the Central 

Valley of California. The RWCP has two primary 

performance goals, specifically, starting with Water 

Year 2002 forward: 

•	Annually provide/deliver Level 2 water supplies 

by specified amounts to the refuges totaling 

422,251 acre-feet; and

•	Annually deliver Incremental Level 4 acquired

water supplies by specified amounts to the 

refuges totaling 133,264 acre-feet.

The RWCP conveys water supplies to the refuges 

using cooperative agreements with water delivery 

entities using Project and acquired water. Established 

refuge allocations for Level 2 and Incremental Level 4

water supplies serve as the Program’s goals for water 

conveyance quantities. 

Reclamation entered into five long-term water 

supply contracts with GWD, FWS, and CDFG which 

established Reclamation’s commitment to the CVPIA

delivery mandates. There contracts are: two with 

CDFG covering Gray Lodge, Los Banos, Volta, 

Mendota and North Grasslands Wildlife Areas; two 

with the FWS covering Sacramento, Delevan, Colusa, 

Sutter, San Luis, Merced, Kern and Pixley National 

Wildlife Refuges; and one with Grassland Water 

District for the Grassland Resource Conservation 

District (GRCD) which is comprised of privately-owned 

and managed wetlands.

Reclamation currently has eight long-term (7-50 years) 

conveyance agreements that are administered by the 

RWCP, along with one FWS 40-year conveyance 

agreement, also administered under the Program. The 

RWCP utilizes cooperative agreements to reimburse 

delivering entities for costs of conveying Level 2 and 

Incremental Level 4 water supplies through Federal,

State, and private water distribution systems to the 

refuges. Conveyance agreements are administered 

out of Reclamation’s South Central California Area 

Office, Northern California Area Office and FWS 

Region 8.

PERFORMANCE MEASURES 

Delivery – The RWCP goal is to deliver Level 2 water 

supplies of 422,251 acre-feet (AF) per year (including 

26,007 AF of replacement water); and Incremental

Level 4 water of 133,264 AF per year.

The RWCP also delivers Level 2 water from non-CVP 

sources to help offset reliance on CVP yield in meeting 

Level 2 requirements.

FY 2011 ACCOMPLISHMENTS 

The program obligated $10,294,003 from the 

Restoration Fund, $3,115,000 from the Water and 

Related Resources Fund, and $70,065 from the BayDelta Fund. 

Refuge Water Conveyance

 3406 (d)(1), (2) and (5)

Egret at Kern National Wildife Refuge
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

Fiscal 

Year* L2 Delivered

% 422,251 AF 

L2 Goal** Inc L4 Delivered

% 133,262 AF 

Inc L4 Goal*** Total Delivery

% Goal 

(555,515 AF)

2002 319,354 76 66,146 50 385,500 69

2003 416,520 99 100,057 75 516,577 93

2004 369,948 88 77,003 58 446,951 80

2005 396,080 94 70,061 53 466,141 84

2006 379,666 90 87,042 65 466,708 84

2007 404,447 96 55,442 42 459,889 83

2008 396,158 94 41,830 31 437,988 79

2009 371,129 88 37,988 29 409,117 74

2010 390,546 92 58,021 44 448,567 81

2011 367,592 87 101,854 76 469,446 85

Average 

Deliveries

381,144 90 69,544 52 450,688 81

* This table reflects deliveries starting with FY 2002, the first year that CVPIA mandated Full Level 4 deliveries for all refuges

 [Section 3046 (d)(2)]. 

** Level 2 goal includes approximately 26,000 AF of replacement water.

*** Incremental Level 4 goal does not include replacement water.

Table 19: Level 2 (L2), Incremental Level 4 (Inc L4) and Full Level 4 Delivery Water by Year, 

2002-2011

Delivery – In 2011, a total of 367,592 AF of Level 2

water was delivered to the refuges, representing 87% 

of the target (Table 19).

A total of 101,854 AF of Incremental Level 4 water

was delivered, representing 76% of the target. 

Table 20 shows the targets and deliveries for each 

refuge for the 2011 Fiscal Year.

Diversification – Of the total of 367,592 AF of Level 

2 water delivered in 2011, a total of 55,343 AF was 

delivered from diverse sources (i.e. non-CVP sources), 

including riparian water rights water, pre-1914 water 

rights water, groundwater, and water provided 

under Merced Irrigation District’s existing mitigation

agreement with the Federal Energy Regulatory 

Commission.

The RWCP co-funded with the RWAP the construction 

of 2 wells at Volta Wildlife Area under the American 

Recovery and Re-investment Act. This project was 

completed in FY 2011. The expected production 

capacity of these wells is approximately 5,000 

acre-feet per year after the first year of production. 

The water will be equally split between Level 2 

diversification and Incremental Level 4 water supplies

Sunset, Sacramento NWR
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 71

REFUGES

Table 20: Water Targets and Deliveries for Each Refuge (FY 2011)

WATER ALLOCATION TARGETS 2011 DELIVERIES % TARGET ACHIEVED***

Refuge Name - 

Region

Level 2 

Water (AF)*

Inc Level 

4 Water 

(AF)**

Full level 4 

Water (AF) 

(= L2+IL4)

Level 2 

Water 

(AF)

Inc Level 

4 Water 

(AF)

Total 

Delivered 

(AF) 

(= L2+IL4)

Level 2 

Water (%)

Inc Level 4 

Water (%)

Full 

level 4 

Water (AF) 

(= L2+IL4)

Grassland Water District (private) — San Joaquin Valley

Grassland RCD 125,000 55,000 180,000 124,577 59,212 183,787 100 108 102

CA Department of Fish and Game — Sacramento Valley

Gray Lodge WA 35,400 8,600 44,000 29,320 0 29,320 83 0 67

CA Department of Fish and Game — San Joaquin Valley

Volta WA 13,000 3,000 16,000 13,220 511 13,731 102 17 86

Los Banos WA 16,670 8,330 25,000 13,925 8,771 22,696 84 105 91

Salt Slough Unit 6,680 3,340 10,020 3,717 5,458 9,175 56 163 92

China Island Unit 6,967 3,483 10,450 3,878 4,721 8,599 56 136 82

Mendota WA 27,594 2,056 29,650 25,076 1,362 26,438 91 66 89

U.S. Fish and Wildlife Service — Sacramento Valley

Sacramento 

NWR 46,400 3,600 50,000 36,562 0 36,562 79 0 73

Delevan NWR 20,950 9,050 30,000 17,834 3,250 21,084 85 36 70

Colusa NWR 25,000 0 25,000 19,912 0 19,912 80 N/A 80

Sutter NWR 23,500 6,500 30,000 15,287 0 15,287 65 0 51

U.S. Fish and Wildlife Service — San Joaquin Valley

San Luis Unit 19,000 0 19,000 16,194 0 16,194 85 N/A 85

Kesterson Unit 10,000 0 10,000 9,340 0 9,340 93 N/A 93

West Bear Creek 

Unit 7,207 3,603 10,810 7,139 3,603 10,742 99 100 99

Freitas Unit 5,290 0 5,290 3,608 0 3,608 68 N/A 68

Merced NWR 13,500 2,500 16,000 11,954 2,500 14,454 89 100 90

East Bear Creek 

Unit 8,863 4,432 13,295 3,055 0 3,055 34 0 23

U.S. Fish and Wildlife Service — Tulare Lake Basin

Kern NWR 9,950 15,050 25,000 12,198 12,468 24,666 123 83 99

Pixley NWR 1,280 4,720 6,000 796 0 796 62 0 13

TOTAL 422,251 133,264 555,515 367,592 101,854 469,446 87 76 85

* This includes approximately 26,000 AF of replacement water.

* * Does not include replacement water

*** The % Target Achieved may exceed 100% because the target levels are for Contract Water Year (March – February) and the water 

deliveries represent volumes delivered during Fiscal Year (October – September).
72 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

Refuges Facilities Construction Actions (RFCA) consists 

of two programs: The Refuge Facilities Construction 

Program (RFCP) and San Joaquin Basin Action Plan 

Lands (SJBAPL) program. Together the RFCA provides 

the necessary infrastructure with sufficient conveyance 

capacity to support long-term delivery of firm, reliable 

water supplies to the boundary of the CVPIA refuges,

as identified in the Central Valley Project Improvement

Act (CVPIA). The RFCP is responsible for the delivery

of water to those lands identified in the Report on 

Refuge Water Supply Investigations (March 1989)

and the SJBAPL program supports the delivery of 

water to the lands specified in the San Joaquin 

Basin Action Plan/Kesterson Mitigation Action Plan 

(December 1989). 

The need to upgrade conveyance facilities is a result of 

capacity constraints in existing delivery systems and/or 

the lack of existing systems. The goal of the RFCA is to 

have the necessary facilities in place for delivery of full 

Level 4 water supplies to the CVPIA refuges, meeting

their timing and scheduling requirements. A full Level 

4 water supply will support optimum wildlife habitat 

over a broad range of species including targeted 

Threatened and Endangered species. 

The RFCA identified 46 major structures and/or 

actions necessary to provide needed capacity for 

the delivery of full Level 4 surface supplies to these 

refuges. These infrastructure improvements can be 

divided into two categories:

•	Modify existing facilities–Existing conveyance 

facilities can be upgraded to overcome 

capacity constraints, and

•	Construct new facilities–New facilities are 

constructed where there is no existing system, or 

where modifications to an existing system would 

not be sufficient to meet demand. 

Twenty of the projects are located on the SJBAPL 

refuge lands. The remaining 26 projects are 

associated with refuges identified in the Report on 

Refuge Water Supply Investigations, Central Valley

Hydrologic Basin, California (March 1989) and are 

implemented through the RFCP. Those refuges still 

requiring conveyance facilities improvements projects 

are: Gray Lodge and Mendota Wildlife Areas, and 

Sutter and Pixley NWRs. 

An Implementation Plan for the SJBAPL was completed

in April 1998, and cooperative agreements with 

the San Luis Canal Company, Grassland Water 

District, and Central California Irrigation District

to convey water to the Action Plan lands were 

completed in summer 1998. Reclamation is currently 

administering the cooperative agreements, which 

include construction and rehabilitation of facilities to 

accommodate the needs of the refuges within San 

Joaquin Basin Action Plan area. 

Program management activities include project 

integration and coordination with the associated 

Refuge Water Conveyance (Wheeling) and Refuge 

Water Acquisition Programs. The objective of this 

activity is to ensure continuity of methodologies and 

approach towards executing and achieving RFCA 

objectives. Interagency coordination activities are

included in this element as well as budget formulation, 

tracking, and management activities. Additional 

activities are administrative coordination for planning, 

design, and construction efforts between agencies 

and water purveyors (water districts). Reclamation 

Mid-Pacific Construction Office (MPCO) provides 

administration of design and construction contracts/

agreements including construction contract award, 

facilities construction activities, construction inspection 

and management, and coordination as appropriate 

with other agencies regarding permit requirements.

Refuge Facilities Construction 

Actions

 3406 (d)(5)
REFUGE FACILITIES CONSTRUCTION AND SAN JOAQUIN BASIN ACTION PLAN LANDS 3406 5)

REFUGES

PERFORMANCE MEASURES 

The goal of the RFCA is to ensure that all 19 CVPIA

refuges have the external conveyance capacity to 

receive Full Level 4 Water, totaling 555,515 acre-feet 

(AF), on an annual basis.

FY 2011 ACCOMPLISHMENTS 

The SJBAPL program obligated $16,680 from the 

Restoration Fund, and $95,294 from the Water and 

Related Resources Fund.

The RFCP obligated $541,900 from the Restoration 

Fund, and $586,351 from the American Recovery and 

Reinvestment Act of 2009.

In FY 2011, the RFCA contracted services for repairs to

the East Bear Pumping Plant. Emergency repairs were 

completed in FY 2011, and pumping was reinitiated on 

the East Bear Creek Unit by September 2011. Nonemergency repairs are expected to be completed in 

FY 2012.

Construction of the Gray Lodge/Pixley Groundwater 

Well Project began in FY 2011 with completion 

expected in FY12. Two wells are under construction 

at Pixley National Wildlife Refuge, and will provide 

for full Level 2 water supplies. Three wells are under 

construction at Gray Lodge Wildlife Area (GLWA), 

and will provide a portion of GLWA’s Level 2 supplies. 

A design contract was executed for the GLWA/BiggsWest Gridley Water District facilities improvement 

project. A value engineering study was completed 

after finalization of concept design. Final design is 

expected to be completed in June 2012. 

The conveyance target by refuge and actual 

conveyance capacity are shown in Table 21.

Snow Geese, Sacramento NWR
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

REFUGES

Table 21: Target Level 4 Conveyance Capacity vs. Actual by Refuge

Refuge Name - Region

Target Level 4 

Capacity 

(in acre-feet)

Actual 

Conveyance 

Capacity (in 

acre-feet) % of Target

Expected Date 

for Completed 

Conveyance 

Construction 

Grassland Water District (private) – San Joaquin Valley

Grassland Resource Conservation District 180,000 180,000 100

CA Department of Fish and Game – Sacramento Valley

Gray Lodge Wildlife Area 44,000 18,000 41 2015

CA Department of Fish and Game – San Joaquin Valley

Volta Wildlife Area 16,000 16,000 100

Los Banos Wildlife Area 25,000 25,000 100

Salt Slough Unit 10,020 10,020 100

China Island Unit 10,450 10,450 100

Mendota Wildlife Area 29,650 26,000 91 2020

U.S. Fish and Wildlife Service – Sacramento Valley

Sacramento National Wildlife Refuge 50,000 50,000 100

Delevan National Wildlife Refuge 30,000 30,000 100

Colusa National Wildlife Refuge 25,000 25,000 100

Sutter National Wildlife Refuge 30,000 0 0 2017

U.S. Fish and Wildlife Service – San Joaquin Valley

San Luis Unit 19,000 19,000 100

Kesterson Unit 10,000 10,000 100

West Bear Creek Unit 10,810 10,810 100

Freitas Unit 5,290 5,290 100

Merced National Wildlife Refuge 16,000 16,000 100

East Bear Creek Unit 13,295 13,295 100

U.S. Fish and Wildlife Service – Tulare Lake Basin

Kern National Wildlife Refuge 25,000 25,000 100

Pixley National Wildlife Refuge 6,000 0 0 2017
Central Valley Project Improvemen

Chapter 5

OTHER

RESOURCE 

AREA
76 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

HABITAT

The Habitat Restoration Program (HRP) benefits 

federally listed Central Valley species and habitats 

impacted by construction and operation of the CVP. 

Habitat loss and fragmentation occurred across 

significant acreage as a result of CVP construction, 

and the program is charged with contributing to the 

habitat mitigation requirements for this loss.

The HRP’s priorities include purchase of fee title or 

conservation easements on lands where threats are 

significant. The program also focuses on restoration 

of CVP-affected habitats, and research to facilitate 

species recovery. In addition, the HRP supports

captive breeding of federally listed species affected by 

the CVP. 

PERFORMANCE MEASURES

Protection and Restoration – The program 

contributes to the protection and restoration of the 2.7 

million habitat acres affected by the construction and 

operation of the CVP. Protection includes both fee title 

acquisition and/or conservation easements.

The 1999 State Water Resources Control Board 

Decision 1641 (SWRCB’s D-1641) requires that 

Reclamation provide compensation and habitat values 

to mitigate for impacts associated with the delivery 

of CVP water to lands previously outside the CVP 

Consolidated Place of Use. It identifies the HRP as one

of three Reclamation programs suitable for fulfilling 

the mitigation plan. Pursuant to the SWRCB’s D-1641, 

Reclamation developed the Consolidated Place of 

Use Habitat Mitigation Plan and Monitoring and 

Reporting Program (HMP) as a report/strategy of how 

the mitigation requirements will addressed. The HMP 

identifies the acquisition, maintenance, and restoration 

of 45,391 acres to occur as mitigation as part of the 

2.7 million affected by the CVP. 

Other Activities – The program also provides funding 

to support the recovery of threatened and endangered 

species through activities such as research, captive 

breeding and outreach. 

FY 2011 ACCOMPLISHMENTS 

The program obligated $1,698,730 from the 

Restoration Fund and $4,151,986 from the Bay-Delta 

Fund to achieve the following: 

Protection and/or Restoration – HRP funding 

helped protect 5,404 acres of land through 

conservation easement acquisitions of 2,407 acres 

of vernal pool, grassland, and riparian habitats at 

the Peek Ranch in Tehama County, and 2,997 acres 

of vernal pool, grassland, and other habitats at the 

Kelsey Ranch in Merced County. Four hundred and 

eighty-one (481) of these acres also count towards 

the State Water Resources Control Board Decision 

1641 acreage (see Table 22 for acres protected and 

restored).

HRP funding helped restore about 28 acres of alkali 

scrub and 101 acres of riparian woodland vegetation 

at the Panorama Vista Preserve in Kern County, and 

492 acres of serpentine grassland and associated 

Habitat Restoration Program

 3406 (b)(1) Other

A conservation easement placed on the vernal pool landscape 

at the Peek Ranch, Tehama County will help protect the 2,407-

acre site.
HABITAT RESTORATION PROGRAM 3406 (b)(1) Othe  

HABITAT

habitats at Santa Teresa County Park in Santa Clara 

County. None of these restored lands contributed 

towards the SWRCB’s D-1641 acreage.

Other Activities – For the second year, the HRP 

provided funds for an effort to map vernal pool habitat 

within the Sacramento and San Joaquin valleys. The 

project will map remaining vernal pool habitat in five 

counties to quantify losses of habitat in core recovery 

areas between 2005 and 2009 (or later). This work 

will contribute to the recovery of federally listed 

species including vernal pool fairy shrimp, vernal pool 

tadpole shrimp, and succulent owl’s clover. For the 

fourth year, the program also contributed funds for the 

captive breeding of the critically endangered Lange’s 

metalmark butterfly. This species is found only at the 

Antioch Dunes National Wildlife Refuge in Contra 

Costa County.

A population of the federally endangered Bakersfield cactus 

grows among the 28 acres of alkali scrub habitat that was 

revegetated at the Panorama Vista Preserve in Kern County.

Year

Acreage 

Protected

Acreage 

Restored

Cumulative 

Acreage 

Progress of 

Protection 

and 

Restoration

1996 3,018 0 3,018

1997 284 617 3,919

1998 74,146 0 78,065

1999 1,180 0 79,245

2000 1,426 206 80,877

2001 2,831 0 83,708

2002 2,211 0 85,919

2003 2,866 0 88,785

2004 719 432 89,936

2005 755 3,370 94,061

2006 193 731 94,985

2007 1,603 122 96,710

2008 1,787 1,908 100,405

2009 5,165 0 105,570

2010 2,049 48 107,667

2011 5,404 621 113,692

Total 105,637 8,055 113,692

Table 22: Acres of Habitat Protected and 

Restored, 1996-2011

Endangered Lange Metalmark butterfly at Antioch Dunes 

National Wildlife Refuge. 
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

HABITAT

The Land Retirement Program (LRP) purchases land, 

water and other property interests from willing sellers 

who receive CVP water. By ceasing irrigation of these 

agricultural lands, the program reduces the volume 

of agricultural drainage produced, and provides the 

opportunity to protect and restore the retired land for 

wildlife habitat.

The Land Retirement Demonstration Project (LRDP) 

was implemented in 1999 at two sites—one in the 

western San Joaquin Valley (Tranquillity, managed by 

Reclamation) and the other in Tulare Lake Basin (Atwell 

Island, managed by the Bureau of Land Management

(BLM))--to study the environmental impacts of land 

retirement and to evaluate cost-effective restoration 

strategies for retired lands. 

PERFORMANCE MEASURES

Retire agricultural land – The program goal is to 

retire (remove from irrigated agriculture) 15,000 acres 

of agricultural lands by 2014 for the Land Retirement 

Demonstration Project. This acreage included the 

acquisition of 7,000 acres at Tranquillity and 8,000 

acres at Atwell Island.

The program has completed its acquisition and 

restoration work in the San Joaquin Valley (Tranquillity 

site). Westlands Water District retired approximately 

100,000 acres, which fulfilled and exceeded the 

goals of the CVPIA land retirement program and

the San Joaquin Valley Drainage Report (1990) for 

acquisition in the San Joaquin Basin. 

The program continues to pursue land retirement at 

the Atwell Island site to fulfill the goal of retirement of

8,000 acres in the Tulare Basin. 

Restore habitat – Restore 400 acres of retired lands 

per year on Land Retirement Demonstration Project 

sites.

Reduce agricultural drainage volume – The 

program cumulatively reduced the production of 

agricultural drainage water by approximately 39,463 

acre-feet through the removal of irrigation water from 

the parcels within the Land Retirement Demonstration 

Project.

FY2011 ACCOMPLISHMENTS 

The program obligated $483,660 from the 

Restoration Fund, and $62,456 from the Water and 

Related Resources Fund. 

Retire agricultural land – Contacts with the 

multiple Atwell Island Project Land owners were

made for the acquisition of the remaining 750 acres. 

However, no land was acquired from willing sellers 

by the program during FY 2011. Table 23 lists the 

cumulative accomplishments of land retirement and 

the annual restoration and ag drainage reduction 

accomplishments.

Restore Habitat – 10,000 pounds of locally grown 

seed from native plants were planted on three-hundred 

acres of previously acquired land at the Atwell Island

site in 2011. An excellent response of annual flora 

was observed at the restoration sites in the spring of FY 

2011, contributing to the ongoing restoration of alkalai 

sink habitat at the site.

Reduce agricultural drainage volume – The 

program reduced the amount of agricultural drainage 

water on LRDP lands by approximately 39,463 acrefeet in FY 2011. 

Other – The BLM is evaluating a proposal from 

a private solar energy developer to construct a 

solar energy production facility at the Atwell Island

Demonstration Project site. Preliminary Biological 

studies were completed in 2011 and BLM is planning 

to start an EIR/EIS in 2012 for the project

Land Retirement Program

 3408 (h)
LAND RETIREMENT PROGRAM 3408 (h) 7

HABITAT

Overall Targets Annual Targets

Acres Acquired Acres Acquired Acres Restored

Reduction in 

Agricultural Drainage 

(acre-feet)

Year

Atwell Island 

(8,000 acres)

Tranquillity*

(7,000 acres) 400 acres 6,000 acre-feet

1995 0 591 0 236

1996 0 0 0 236

1997 0 0 0 236

1998 0 995 1,220 634

1999 0 60 100 658

2000 2,645 0 777 1,716

2001 1,414 444 702 1,992

2002 1,510 0 373 2,672

2003 616 0 261 2,772

2004 155 0 308 3,000

2005 625 0 349 3,340

2006 38 0 416 3,355

2007 213 0 475 3,440

2008 0 0 390 3,568

2009 0 0 380 3,728

2010 50 0 400 3,888

2011 0 0 260 3,992

Total 7,266 2,090 6,411 39,463** 

 * Land acquisition at the Tranquility site was deemed complete in 2001 with the retirement of approximately 100,000 acres of

 drainage problem lands by the Westlands Water District. Acreage shown reflect only USBR acquired lands. 

** Reduction in Agricultural Drainage Total is cumulative from 1995 - 2011.

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2011
80 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

HABITAT

While not typically considered part of the resource 

areas , CVPIA Contract Renewals and Water Transfers

are in fact a provision under the administration of the 

CVPIA. A brief summary of their accomplishments is

discussed below.

CONTRACT RENEWALS 

(3404(c))

Section 3404(c) of the Central Valley Project 

Improvement Act authorized and directed the

Secretary to renew repayment and water service 

contracts for the delivery of water from the Central 

Valley Project (CVP). Since the passage of the Act, 

Reclamation has and continues to execute renewal 

contracts for the continued delivery of CVP water. 

To date, 88 long term renewal contracts and 27 

interim-renewal contracts have been executed within 

the various divisions of the CVP. There are 4 contracts 

that have completed negotiation for a long term 

contract, and 1 currently in long term negotiations. In

addition, 132 long term contracts have been renewed 

with the Sacramento River Water Right Settlement 

contractors and 1 is pending renewal upon expiration 

in July 2020. Reclamation will continue to implement 

interim contract renewal consistent with CVPIA until

such time that all environmental requirements have 

been satisfied, including the completion of a new 

biological opinion on the overall operations of the 

CVP. At that time, Reclamation intends to complete 

long term contract renewal.

WATER TRANSFERS (3405)

Water transfers are a means by which existing water 

supplies can be reallocated from one user to another 

to assist in meeting existing and future water needs 

within California. Water transfers represent an 

important management option because they create 

opportunities to meet municipal, industrial demands, as 

well as benefit environmental and recreational values. 

Under Section 3405, CVPIA authorizes individuals

and districts who received CVP water to transfer all or 

a portion of that water to other users within the state 

for any purpose recognized as beneficial under state 

law, subject to certain terms and conditions. 

Reclamation has approved the transfer of CVP water in 

the following categories for FY 2011: 

•	566,845 AF of CVP agricultural water was 

approved for agricultural purposes

•	6,870 AF of CVP agricultural water was 

approved for agricultural purposes (Recaptured 

Water Account (RWA))

•	270,000 AF of CVP agricultural water was 

approved for municipal and industrial purposes 

(Metropolitan Water District)

•	1,200 AF of CVP municipal and industrial water 

was approved for agricultural purposes

•	2,200 AF of CVP municipal and industrial water 

was approved for municipal and industrial 

purposes

•	675 AF of CVP municipal and industrial water 

was approved for municipal and industrial 

purposes (Recaptured Water Account (RWA))

•	50,333 AF of CVP agricultural water approved 

to Reclamation’s Refuge Water Acquisition 

Program 

These records are normally maintained on a contract 

year basis, March 1 to February 28 (the contract 

year is designated by the year in which it begins). 

Therefore, the stated amounts will differ from other 

numbers reported for the contract year.

Contract Renewals and Water 

Transfers

 3404 (c) and 3405
APPENDICES 8

Central Valley Project Improvemen

APPENDICES
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2011 

Accomplishments Comments

FISHERIES

ANADROMOUS FISH RESTORATION PROGRAM (AFRP), 3406 (b)(1)

Double the number of naturally produced, 

Central Valley wide, Fall-run Chinook

750,000 fish 1992 - 2011 

average

372,344 50 102,821

Double the number of naturally produced, 

Central Valley wide, Late Fall-run Chinook

68,000 fish 1992 - 2011 

average

18,383 27 5,577

Double the number of naturally produced, 

Central Valley wide, Winter-run Chinook

110,000 fish 1992 - 2011 

average

6,578 6 1,552

Double the number of naturally produced, 

Central Valley wide, Spring-run Chinook

68,000 fish 1992 - 2011 

average

14,091 21 2,064

Double the number of Central Valley wide 

Green Sturgeon

2,000 fish 1992 - 2005 

average

2,948 147 10,272 Last data submission was 2009. 

Data provided from CDFG in 2006 

- 2009 is preliminary amd not 

used in calculation

Double the number of Central Valley wide 

15-year old, White Sturgeon

11,000 fish 1992 - 2005 

average

6,237 57 6258 Last data submission was 2009. 

Data provided from CDFG in 

2006 - 2009 is preliminary amd 

not used in calculation

Double the number of Central Valley wide 

Striped Bass

2,500,000 fish 1992 - 2007 

average

978,199 39 684,486 Data from 2010

Double the number of Central Valley wide 

American Shad

4,300 fish 1992-2009 

average

2,468 57 683 Last data year 2009

Cubic Yards of Spawning gravel placed in 

the American, Merced, and/or Tuolumne 

rivers.

unspecified Annual 39,000 N/A 39,000

Tons of Spawning gravel placed in the 

Mokelumne River

unspecified Annual 6,557 N/A 6,557

Complete 105 structural actions 105 actions Cumulative 63 60 10

Contribute towards completion of 128 High 

and Medium Priority Actions

128 actions Cumulative 45 35 0

DEDICATED PROJECT YIELD, 3406 (b)(2)

Provide instream flow, specified based on 

Wet, Dry, or Critically Dry year.

Wet Year target is 

800,000 acre-feet

Annual 800,000 100 800,000 2011 Water Year was classified 

Wet

WATER ACQUISITION - INSTREAM, 3406 (b)(3)

Provide supplemental (b)(2) instream flow 

water

200,000 acre-feet Average 

from 1994 - 

2011

80,956 40 38,500 FY2011 acquired water is 19.25% 

of target

TRACY PUMPING PLANT/TRACY FISH TEST FACILITY, 3406 (b)(4)

Complete 23 actions to mitigate for fishery 

impacts

23 mitigation 

actions

Cumulative 16 70 0

Appendix A: Progress to Date 

Toward CVPIA Performance 

Goals
APPENDIX A: PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOAL  

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2011 

Accomplishments Comments

CONTRA COSTA CANAL PUMP, 3406 (b)(5)

Complete structural actions to mitigate for 

fishery impacts (fish screen and pumping 

plant)

Complete the 

fish screen and 

pumping plant 

modifications

Cumulative Completed 100 Completed

RED BLUFF DIVERSION DAM, 3406 (b)(10)

Increase the Fish Passage Rate of Adult 

Spring-run Chinook

80-100% Annual 80% 100 80% Within target range

Increase the Fish Passage Rate of Adult 

Green Sturgeon

50-100% Annual 75% 100 75% Within target range

Complete the fish screen and pumping 

plant

100% Cumulative 65% 65 40%

CLEAR CREEK RESTORATION, 3406 (b)(12)

Restore stream channel 2 miles Cumulative 1.5 75 0.0

Place spawning gravel annually 17,000 tons Annual 10,000 59 10,000

Meet variable flow target Annual 100 Ongoing operation

Maintain water temperature for optimum 

anadromous fish production

Maintain proper 

temperature 

100% of the time

Annual 88% 88 60°F 1-Jun to 14-Sep

56°F 15-Sep to 31-Oct

SPAWNING GRAVEL, 3406 (b)(13)

Place 10,000 tons of spawning gravel 

annually in the Sacramento River.

10,000 tons Annual 5,000 50 5,000

Place 3,000 tons of spawning gravel 

annually in the Stanislaus River

3,000 tons Annual 5,000 167 5,000

Place 7,000 tons of spawning gravel 

annually in the American River

7,000 tons Annual 20,770 297 20,770

Increase the percentage of spawning 

salmonids using placed gravel in the 

Sacramento River

25% usage Annual 6% 24% 6% 

Increase the percentage of spawning 

salmonids using placed gravel in the 

Stanislaus River

10% usage Annual 21% 210% 21%

Increase the density of redds on emplaced 

gravel in the American River

0.03 redds/sq. 

meter

Annual 0.01 33 0.01

OLD RIVER BARRIER, 3406 (b)(15)

Construct fishbarrier at Head of Old River 1 structural action 

completed

Cumulative 0 0 0 A temporary bubble barrier was 

installed in 2009 and 2010, but 

could not be deployed in 2011

Operate a fish barrier at Head of Old River 100% of fish 

blocked

Annual 0 0 0 Temporary barrier deployed in 

2010 bloked 100% of fish

COMPREHENSIVE ASSESSMENT AND MONITORING PROGRAM, 3406 (b)(16)

Create an Annual Report 1 Annual Report Annual 1 100 1

Management of CVPIA data Unspecified Annual N/A N/A N/A

ANADROMOUS FISH SCREENS PROGRAM (AFSP), 3406 (b)(21)

Screen all high priority diversions on 

prescribed streams

Unspecified Cumulative 33 Undefined 4

TRINITY RIVER RESTORATION PROGRAM (TRRP), 3406 (b)(23)

Increase the escapment of Hatchery 

produced Fall-run Chinook Salmon

9,000 fish 1992 - 2010 

Average

8,953 99 18,827 Values provided are based on 

2010 data

Increase the escapment of Naturally 

produced Fall-run Chinook Salmon

62,000 fish 1992 - 2010 

Average

20,876 34 14,188 Values provided are based on 

2010 data

Increase the escapment of Hatchery 

produced Spring-run Chinook Salmon

3,000 fish 1992 - 2010 

Average

3,880 129 9,285 Values provided are based on 

2010 data

Increase the escapment of Naturally 

produced Spring-run Chinook Salmon

6,00 fish 1992 - 2010 

Average

4,477 75 5,483 Values provided are based on 

2010 data
84 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2011 

Accomplishments Comments

Increase the escapment of Hatchery 

produced Coho Salmon

2,100 fish 1992 - 2010 

Average

5,852 279 12,282 Values provided are based on 

2010 data

Increase the escapment of Naturally 

produced Coho Salmon

1,400 fish 1992 - 2010 

Average

817 58 1,890 Values provided are based on 

2010 data

Increase the escapment of Hatchery 

produced Steelhead

10,000 fish 1992 - 2010 

Average

4,640 46 12,556 Values provided are based on 

2010 data

Increase the escapment of Naturally 

produced Steelhead

40,000 fish 1992 - 2010 

Average

3,811 10 4,170 Values provided are based on 

2010 data

Improve Infrastructure to allow ROD flows 

(369 TAF - 815 TAF)

Unspecified Annual Within target 100

Provide minimum annual flows. The 

program releases between 369,000 and 

815,000 AF each year, in accordance with 

the ROD

Volume target 

and peak flow 

varies by water 

year type

Annual 701,000 103 721,800 Based on 2011 as a wet water 

year

TRINITY RIVER RESTORATION PROGRAM (TRRP), 3406 (b)(1) Other

Complete 47 channel rehabilitation projects 

in the Trinity mainstem and 3 side channels

47 projects Cumulative 24 51 1

Place 10,000 cubic yards of coarse 

sediment annually

10,000 cubic 

yards

Annual 5,300 53 5,300

Reduce fine sediment delivery from 

tributary watersheds

10,000 to 20,000 

cubic yards

Annual 9,600 96 9,600

SAN JOAQUIN RIVER RESTORATION PLAN (SJRRP), 3406 (c) (1)

Reduce or avoid water supply impacts to 

Friant Division long-term contractors

Unspecified Annual 106,318 Undefined 106,318

Restore and maintain fish populations in 

good condition

“Good” condition Annual

ECOLOGICAL AND WATER SYSTEMS MODELS, 3406 (g)

Develop readily usable and broadly 

available hydrologic and ecologic models 

and supporting data to evaluate existing 

and alternative water management 

strategies

9 hydrologic/

ecologic models

Cumulative 8 89 0

CVP WATER OPERATIONS

RESERVOIR STORAGE, 3406 (b)(19)

Maintain minimum reservoir storage in 

Shasta Reservoir

19 MAF Cumulative 12 of 14 86 3.3 MAF

Maintain minimum reservoir storage in 

Trinity Reservoir

600 TAF Cumulative 14 of 14 100 2.167 TAF

REFUGES

REFUGE WATER SUPPLY PROGRAM - ACQUISITION (INC L4), 3406 (b)(3) and 3406(d)(2)

Acquire 133,264 acre-feet for Incremental 

Level 4 water acquisition

133,264 acre-feet Annual 97,997 74 97,997

REFUGE WATER SUPPLY PROGRAM - CONVEYANCE, 3406 (d)(1)

Provide Level 2 water supplies 422,251 acre-feet Annual 367,592 87 367,592 Target includes 26,007 acre-feet 

of replacement water

REFUGE WATER SUPPLY PROGRAM - CONVEYANCE, 3406 (d)(2)

Provide incremental Level 4 water supplies 133,264 

acre-feet

Annual 101,854 76 101,854

REFUGE WATER SUPPLY PROGRAM - CONSTRUCTION (FULL L4 CAPACITY), 3406 (d)(5)

Provide external conveyance capacity to 

19 refuges to receive Full Level 4 Water 

annually

555,515 acre-feet Cumulative 489,865 88 0

REFUGE WATER SUPPLY PROGRAM - CONSTRUCTION (PLANNING, DESIGN & CONSTRUCTION), 3406 (d)(5)

Planning, design & construction to deliver 

water to 19 Refuges

19 refuges 

with adequate 

conveyance

Cumulative 15 79 1 E. Bear Unit complete
APPENDIX A: PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOAL  

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2011 

Accomplishments Comments

OTHER

HABITAT RESTORATION, 3406 (b)(1) Other

Protect and/or restore habitat impacted by 

the CVP

A portion of 

2,700,000 acres

Cumulative 113,692 TBD 6,025 Exact portion of target is yet to be 

determined

Protect and/or restore habitat areas 

specified by the SWRCB Decision 1641

45,391 acres Cumulative 7,159 16 481

LAND RETIREMENT, 3408(h)

Retire 8,000 acres of Atwell Island land 8,000 acres Cumulative, 

1995–2011

7,266 91 0

Retire 7,000 acres of Tranquility land Complete Cumulative, 

1995–2011

7,000 100 N/A

Restore 400 acres of retired land annually 400 acres Cumulative, 

1995–2011

6,411 76 260

Reduce the production of agricultural 

drainage water by 6,000 AF through the 

removal of irrigation water from the parcels 

within the Land Retirement Demonstration 

Project

6,000 acre-feet Cumulative, 

1995–2011

39,463 67 104 3,992 AF reduced over 21 years 

on 9,980 acres of land
86 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

AF acre-feet 

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program Team

ARRA American Recovery and Reinvestment Act

ATR Annual Technical Report

BDCP Bay Delta Conservation Plan

BLM Bureau of Land Management 

BMP Best Management Practices

BO Biological Opinion

CAMP Comprehensive Assessment Monitoring 

Program

CALFED CALFED Bay-Delta Program 

CCWD Contra Costa Water District Statement

CDFG California Department of Fish and Game 

CPAR CVPIA Program Activity Review Statemen

CVP Central Valley Project

CVPIA Central Valley Project Improvement A

CY contract year

DHCCP Delta Habitat Conservation and Conveyance 

Program

DOI Department of the Inter

DWR Department of Water Resources

ECOSIM Ecology Cogent Operations Suite

of Integrated Model

EDT Ecosystem Diagnostic and Treatment

EIR Environmental Impact Repo

EIS Environmental Impact Stateme

ESA Endangered Species Act

EWSOMP Ecosystem and Water Systems 

Operations Models Program

FWS US Fish and Wildlife Service 

FWUA Friant Water Users Authority

FY Fiscal year

GCID Glenn-Colusa Irrigation Distri

GWD Grassland Water District

HGS HydroGeoSphere

HRP Habitat Restoration Plan

IFIM Instream Flow Incremental Method

Interior Department of the Interi

IP Implementation P

IRWMT Interagency Refuge Water Managem

LRP Land Retirement Program

NMFS National Marine Fisheries Service 

NOAA National Oceanic Atmospheric 

Administration

NRDC Natural Resources Defense Council

NWR National Wildlife Refuge 

OCAP Operating Criteria and Procedures

OMB Office of Management and Budget 

PART Program Assessment Rating Tool

PEIS Programmatic Environmental Impa

PIMS Performance Information Manageme

POD Pelagic Organism Decline

RBDD Red Bluff Diversion Dam

RHEM Riparian Habitat Establishment Model

ROD Record of Decision

RPA Reasonable and Prudent Action

RST Rotary Screw Trap

RWSP Refuge Water Supply Program

SJBAPL San Joaquin Basin Action Plan Lands

SJBAP San Joaquin Basin Action Plan 

SJRA San Joaquin River Agreement 

SJRGA San Joaquin River Group Authority

SJRR San Joaquin River Restoration

SMUD Sacramento Municipal Utility District

SNWR Sacramento National Wildlife Refuges

SWP State Water Project

TFCF Tracy Fish Collection Facility 

TRRP Trinity River Restoration Program

US United States

Appendix B: Acronyms
APPENDIX C: GLOSSARY OF TERMS 8

• Acre-foot (AF)

The quantity of water required to cover one 

acre to a depth of one foot: equal to 1,233.5 

cubic meters (43,560 cubic feet)

• Anadromous fish

Those stocks of salmon (including other species, 

e.g., steelhead, striped bass, white and green 

sturgeon, and American shad) that ascend the 

Sacramento and San Joaquin rivers and their 

tributaries and the Sacramento-San Joaquin 

Delta to reproduce after reaching maturity in San 

Francisco Bay or the Pacific Ocean; fish species 

that spend most of their lives in the ocean but 

reproduce in fresh water 

• Anadromous Fish Restoration Program 

(AFRP)

A program authorized by the CVPIA to address

anadromous fish resource issues in Central Valley 

streams that are tributary to the Delta 

• Biota

Total collection of organisms of a geographic 

region or a time period

• CALFED Bay-Delta Program

A unique collaboration among 25 state and 

federal agencies that came together to improve 

California’s water supply and the ecological 

health of the San Francisco Bay/Sacramento-San 

Joaquin River Delta 

• Capillary rise

Movement of water upwards from the watertable 

(the top of the groundwater) into the unsaturated 

soil above; can be likened to a dry sponge (the 

unsaturated soil) being placed on top of a wet 

surface (the watertable), the sponge sucking up 

water being similar to capillary rise in soils

• Central Valley

Area in the central portion of California bounded 

by the Cascade Range to the north, the Sierra 

Nevada to the east, the Tehachapi Mountains to 

the south and the coast ranges and San Francisco 

Bay to the west

• Central Valley Project (CVP)

As defined by Section 3403(d) of the CVPIA,

“all Federal reclamation projects located within 

or diverting water from or to the watershed of 

the Sacramento and San Joaquin rivers and their 

tributaries as authorized by the Act of August 26, 

1937 (50 Stat. 850) and all Acts amendatory or 

supplemental thereto, ...”

• Central Valley Project water

As defined by Section 3403(f) of the CVPIA,

“all water that is developed, diverted, stored, 

or delivered by the Secretary in accordance 

with the statutes authorizing the Central Valley 

Project in accordance with the terms and 

conditions of water rights acquired pursuant to 

California law.”

• Central Valley Project Improvement Act 

(CVPIA)

Public Law 102-575, Title 34. This law was 

passed in 1992 for the following purposes: 

a. Protect, restore, and enhance fish, wildlife, 

and associated habitats in the Central 

Valley and Trinity River basins of California 

b. Address impacts of the Central Valley 

Project on fish, wildlife and associated 

habitats 

c. Improve the operational flexibility of th

Central Valley Project 

d. Increase water-related benefits provide

by the Central Valley Project to the State 

of California through expanded use of 

voluntary water transfers and improved water 

conservation 

e. Contribute to the State of California’s interim 

and long-term efforts to protect the San 

Appendix C: Glossary of Terms
88 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Francisco Bay/Sacramento-San Joaquin 

Delta Estuary 

f. Achieve a reasonable balance among 

competing demands for use of Central Valley 

Project water, including the requirements of 

fish and wildlife, agricultural, municipal and 

industrial and power contractors

• Central Valley Habitat Joint Venture 

(CVHJV)

The association of federal and state agencies 

and private parties established for the purpose 

of developing and implementing the North 

American Waterfowl Management Plan as it 

pertains to the Central Valley of California

• Central Valley Rivers and Streams

The 22 Central Valley main rivers and streams 

were defined in the January 9, 2001, Final 

Restoration Plan, Appendix B as: Sacramento 

River, Clear Creek, Cow Creek, Cottonwood 

Creek, Battle Creek, Paynes Creek, Antelope 

Creek, Mill Creek, Deer Creek, Miscellaneous 

creeks, Butte Creek, Big Chico Creek, Feather 

River, Yuba River, Bear River, American River, 

Mokelumne River, Cosumnes River, Calaveras 

River, Stanislaus River, Tuolumne River, and 

Merced River.

• Constant fractional marking program (CFM)

When fish are counted for CVPIA monitoring,

program managers differentiate between wild 

and hatchery fish; hatcheries mark a percentage 

of juveniles before they are released and when 

fish come back to spawn, the mark will indicate 

which were hatchery-born

• Diversion

Area where river water is rerouted in a direction 

other than its natural course

• Entrainment

When fish are diverted from their natural 

spawning course (e.g., caught in a water pump or 

diverted from the river into a canal)

• Environmental Impact Statement (EIS)

An analysis required by the National 

Environmental Policy Act (NEPA) for all 

major federal actions, which evaluates the 

environmental risks of alternative actions 

• Escapement

Measurement of adult spawning anadromous 

fish (e.g., salmon) that manage to return to their 

spawning stream

• Firm water supplies

Non-interruptible water supplies guaranteed by 

the supplier to be available at all times except for 

reasons of uncontrollable forces or continuity of 

service provisions 

• Flow

The volume of water passing a given point per 

unit of time, usually in cubic feet per second (cfs)

• Habitat

Area where a plant or animal lives

• Level 2

A term used to refer to refuge water supply 

deliveries; the 1989 and 1992 Refuge Water 

Supply Studies define Level 2 refuge water 

supplies as the average amount of water the 

refuges received between 1974 and 1983

• Level 4

A term used to refer to refuge water supply 

deliveries; Level 4 refuge water supplies are 

defined in the 1989 and 1992 Refuge Water 

Supply Studies as the amount of water for 

full development of the refuges based upon 

management goals developed in the 1980s

• Measure

A type of program activity defined by the 

provisions of CVPIA that includes specific physical

or structural actions

• Metric

The defined quantifiable measurement of outputs 

or outcomes

• Mitigation

One or all of the following: (1) Avoiding an 

impact by not taking a certain action or parts 

of an action; (2) minimizing impacts by limiting 

the degree or magnitude of an action and 

its implementation; (3) rectifying an impact 

by repairing, rehabilitating, or restoring the 

affected environment; (4) reducing or eliminating 

an impact over time by preservation and 

maintenance operations during the life of an 

action; and (5) compensating for an impact by 
APPENDIX C: GLOSSARY OF TERMS 8

replacing or providing substitute resources or 

environments

• Natural Production

As defined by Section 3403(h) of the CVPIA,

“fish produced to adulthood without direct human 

intervention in the spawning, rearing, or migration 

processes”

• Outcome

The intended results or consequences to be 

achieved through implementing measures and 

programs described in the CVPIA

• Output

The specific actions, measures, programs and 

services produced by Reclamation and the 

Service and provided to the public or others; 

outputs are the activities of the CVPIA Program

to achieve the outcomes defined by the Act or 

developed by Reclamation and the Service to 

achieve the environmental restoration purposes

• Pelagic Organism Decline

A recent decline in both abundance and species 

richness of pelagic (living in water above the 

bottom) organisms within the Sacramanto-San 

Joaquin Delta; pelagic organisms include, 

most notably, the delta smelt and longfin smelt, 

federally-listed endangered species of fish

• Program

The overall effort to implement the provisions of 

CVPIA

• Program Activity

The individual provisions of CVPIA that are

being implemented by “program managers” at 

Reclamation and the Service

• Program Manager

The staff at Reclamation and the Service that 

oversees implementation of the CVPIA program

activities; each active program activity has a 

program manager from its respective agency

• Redd Dewatering

Occurs when redds (fish egg “nests”) are left 

exposed by receding water levels

• Restoration Fund

The fund established by Section 3407 of 

the CVPIA to contribute resources for the

environmental restoration provisions of the Act; 

revenue comes into the fund primarily through 

surcharges on water and power contract rates

• Restoration Fund Roundtable

A collective of stakeholders representing 

environmental organizations, federal and state 

resource agencies, water and power contractors, 

and other interested parties who meet as needed 

to discuss issues, news and activities related to the 

Central Valley Project Improvement Act (CVPIA

and provide information to Reclamation and the 

Service

• Riparian

Of or relating to or located on the banks of a 

river or stream

• South Delta

Sacramento-San Joaquin Delta

• Stranding

Stranding is a term used to describe fish that 

are trapped in pools of water that have no 

connectivity to the larger stream because of 

insufficient flow

• Target

The quantifiable or otherwise measurable 

characteristics that tell how well a program must 

accomplish a performance measure. 

• Taxa

Designating an organism or group of organisms

• Timeframe

The period of time when program activities occur 

(e.g., annual or long term) that combine with a 

performance measure and target, establish a 

performance goal

• Water Acquisition

The purchase of water from willing sellers

• Weir

Type of fish ladder that utilizes a series of small 

dams and pools to create a long channel and 

allow spawning fish to get around an obstruction, 

like a dam

• WY

Water year
90 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Appendix D: CVPIA Title 34 of 

Public Law 102-575

SECTIONS

Anadromous Fish Restoration 

Program – Section 3406 (b)(1)

“The Secretary ... is authorized and directed to 

... develop within three years of enactment and 

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 longterm basis, at levels not less than twice the average 

levels, attained during the period of 1967-1991.” 

The section also states, “this goal shall not apply 

to the San Joaquin River between Friant Dam and 

the Mendota Pool, for which a separate program 

is authorized under subsection 3406(c) of this 

title; Provided further, That the programs and 

activities authorized by this section shall, when fully 

implemented, be deemed to meet the mitigation, 

protection, restoration, and enhancement purposes 

established by subsection 3406(a) of this title; And 

provided further, That in the course of developing 

and implementing this program the Secretary 

shall make all reasonable efforts consistent with 

the requirements of this section to address other 

identified adverse environmental impacts of the 

Central Valley Project not specifically enumerated in 

this section.”

Habitat Restoration Program – Section 

3406 (b)(1) “other”

“...in the course of developing and implementing 

this program the Secretary shall make all 

reasonable efforts consistent with the requirements 

of this section to address other identified adverse 

environmental impacts of the CVP not specifically 

enumerated in this section.”

Trinity River Restoration Program – Section 3406(b)

(1) “other” and 3406(b)(23)

“...That in the course of developing and 

implementing this program the Secretary shall 

make all reasonable efforts consistent with the 

requirements of this section to address other 

identified adverse environmental impacts of the 

Central Valley Project not specifically enumerated in 

this section”; and 

“In order to meet Federal trust responsibilities to 

protect the fishery resources of the Hoopa Valley 

Tribe, and to meet the fishery restoration goals of the 

Act of October 24, 1984, Pub. L. 98-541, provide 

through the Trinity River Division, for water years 

1992 through 1996, an instream release of water 

to the Trinity River of not less than 340,000 acrefeet per year for the purposes of fishery restoration, 

propagation, and maintenance...”

Modified CVP Operations – Section 

3406 (b)(1)(B)

“As needed to achieve the goals of this program, 

the Secretary is authorized and directed to modify 

CVP operations to provide flows of suitable quality, 

quantity, and timing to protect all life stages of 

anadromous fish, except that such flows shall be 

provided from the quantity of water dedicated 

to fish, wildlife, and habitat restoration purposes 

under paragraph (2) of this subsection; from the 

water supplies acquired pursuant to paragraph (3) 

of this subsection; and from other sources which 

do not conflict with the fulfillment of the Secretary’s 

remaining contractual obligations to provide CVP 

water for other authorized purposes. Instream 

flow needs for all Central Valley Project controlled 

streams and rivers shall be determined by the 

Secretary based on recommendations of the U.S. 

Fish and Wildlife Service after consultation with the 

California Department of Fish and Game.”

Dedicated 800,000 acre-feet Project 

Yield – Section 3406 (b)(2)

“...dedicate and manage annually 800,000 

acre-feet of Central Valley Project yield for the 

primary purpose of implementing the fish, wildlife, 

and habitat restoration purposes and measures 
APPENDIX D: CVPIA TITLE 34 OF PUBLIC LAW 102-  

authorized by this title; 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 such obligations as may 

be legally imposed upon the Central Valley Project 

under state or federal law following the date of 

enactment of this title, including but not limited to 

additional obligations under the federal Endangered 

Species Act...”

Water Acquisition Program - Instream 

Water – Sections 3406 (b)(3) and 

3406 (g)

“The Secretary ... is authorized and directed to 

develop and implement a program in coordination 

and in conformance with the plan required under 

paragraph (1) of this subsection for the acquisition 

of a water supply to supplement the quantity of 

water dedicated to fish and wildlife purposes under 

paragraph (2) of this subsection.... The program 

should identify how the Secretary intends to utilize, 

in particular the following options: improvements 

in or modifications of the operations of the project; 

water banking; conservation; transfers; conjunctive 

use; and temporary and permanent land fallowing, 

including purchase, lease, and option of water, water 

rights, and associated agricultural land.”

Tracy (Jones) Pumping Plant Program 

– Section 3406 (b)(4)

“Develop and implement a program to mitigate for 

fishery impacts associated with operations of the 

Tracy Pumping Plant. Such program shall include, 

but is not limited to improvement or replacement 

of the fish screens and fish recovery facilities and 

practices associated with the Tracy Pumping Plant.”

Contra Costa Canal Pumping Plant - 

Section 3406 (b)(5)

“...Develop and implement a program to mitigate 

for fishery impacts resulting from operations of 

the Contra Costa Canal Pumping Plant No. 1. 

Such a program shall provide for construction and 

operation of fish screening and recovery facilities, 

and for modified practices and operations.”

Flow Fluctuations and Reservoir 

Storage – Section 3406 (b)(9) and 

(b)(19)

“(9) Develop and implement a program to eliminate, 

to the extent possible, losses of anadromous fish due 

to flow fluctuations caused by the operation of 

any Central Valley Project storage or re-regulating 

facility...”

 “(19) Reevaluate existing operational criteria in 

order to maintain minimum carryover storage at 

Sacramento and Trinity River reservoirs to protect 

and restore the anadromous fish of the Sacramento 

and Trinity Rivers in accordance with the mandates 

and requirements of this subsection and subject 

to the Secretary’s responsibility to fulfill all project 

purposes, including agricultural water delivery.”

Red Bluff Diversion Dam – 

Section 3406 (b)(10)

“Develop and implement measures to minimize 

fish passage problems for adult and juvenile 

anadromous fish at Red Bluff Diversion Dam...”

Clear Creek Restoration Program – 

Section 3406 (b)(12)

“Develop and implement a comprehensive 

program to provide flows to allow sufficient 

spawning, incubation, rearing, and outmigration 

for salmon and steelhead from Whiskeytown Dam 

as determined by instream flow studies conducted 

by the California Department of Fish and Game 

after Clear Creek has been restored and a new fish 

ladder has been constructed at the McCormickSaeltzer Dam...”

Spawning and Rearing Habitat 

Restoration Program – Section 3406 

(b)(13) 

“Develop and implement a continuing program 

... to restore and replenish spawning gravel...

and rearing habitat ... on the American, Stanislaus 

and Sacramento Rivers ... shall include preventive 

measures...”

Head of Old River Barrier – Section 

3406 (b)(15)

“Construct, in cooperation with the State of 

California and in consultation with local interests, a 

barrier at the head of Old River in the SacramentoSan Joaquin Delta to be operated on a seasonal 

basis to increase the survival of young outmigrating 

salmon that are diverted from the San Joaquin River 

to Central Valley Project and State Water Project 

pumping plants and in a manner that does not 

significantly impair the ability of local entities to 

divert water...”
92 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2011 ANNUAL REPO

Comprehensive Assessment and 

Monitoring Program – Section 3406 

(b)(16)

“...Establish, in cooperation with independent 

entities and the State of California, a comprehensive 

assessment program to monitor fish and wildlife 

resources in the Central Valley to assess the 

biological results and effectiveness of actions 

implemented pursuant to this subsection....”

Anadromous Fish Screen Program – 

Section 3406 (b)(21)

“Assist the State of California in efforts to develop 

and implement measures to avoid losses of juvenile 

anadromous fish ... measures shall include but 

shall not be limited to construction of screens on 

unscreened diversions, rehabilitation of existing 

screens, replacement of existing non-functioning 

screens, and relocation of diversions to less fisherysensitive areas.”

San Joaquin River Restoration 

Program – Section 3406 (c)(1)

“The Secretary shall ” ... develop a comprehensive 

plan which is reasonable, prudent, and feasible 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 sustain naturally 

reproducing anadromous fisheries from Friant 

Dam to its confluence with the San Francisco Bay/

Sacramento-San Joaquin Delta Estuary.”

Refuge Water Supply Program – 

Section 3406 (b)(3), 3406 (d)(1), 

3406 (d)(2), 3406 (d)(5)

“3406 (b)(3) Develop and implement a program 

in coordination and in conformance with the plan 

required under paragraph (1) of this subsection 

for the acquisition of a water supply to supplement 

the quantity of water dedicated to fish and wildlife 

purposes under paragraph (2) of this subsection and 

to fulfill the Secretary’s obligations under paragraph 

3406(d)(2) of this title....”

“3406 (d)(1)Upon enactment of this title, the quantity 

and delivery schedules of water measured at the 

boundaries of each wetland habitat area described 

in this paragraph shall be in accordance with Level 2 

of the “Dependable Water Supply Needs” table for 

those habitat areas as set forth in the Refuge Water 

Supply Report and two-thirds of the water supply 

needed for full habitat development for those habitat 

areas identified in the “San Joaquin Basin Action 

Plan/Kesterson Mitigation Action Plan Report...”

“3406 (d)(2) Not later than ten years after enactment 

of this title, the quantity and delivery schedules of 

water measured at the boundaries of each wetland 

habitat area described in this paragraph shall be in 

accordance with Level 4 of the “Dependable Water 

Supply Needs” table for those habitat areas as set 

forth in the “Refuge Water Supply Report” and the 

full water supply needed for full habitat development 

for those habitat areas identified in the “San Joaquin 

Basin Action Plan/Kesterson Mitigation Action Plan 

Report...”

“3406 (d)(5) The Secretary is authorized and 

directed to construct or to acquire from non-Federal 

entities such water conveyance facilities, conveyance 

capacity, and wells as are necessary to implement 

the requirements of this subsection; provided, that 

such authorization shall not extend to conveyance 

facilities in or around the Sacramento-San Joaquin 

Delta Estuary...”

Ecosystem and Water Systems 

Operations Models – Section 3406 (g)

“The Secretary, in cooperation with the State of 

California and other relevant interests and experts, 

shall develop readily usable and broadly available 

models and supporting data to evaluate the ecologic 

and hydrologic effects of existing and alternative 

operations of public and private water facilities and 

systems in the Sacramento, San Joaquin, and Trinity 

River watersheds. The primary purpose of this effort 

shall be to support the Secretary’s efforts in fulfilling 

the requirements of this title through improved 

scientific understanding concerning, but not limited 

to, the following:

(1) a comprehensive water budget of surface and 

groundwater supplies, considering all sources 

of inflow and outflow available over extended 

periods;

(2) related water quality conditions and improvement 

alternatives, including improved temperature 

prediction capabilities as they relate to storage;

(3) surface-ground and stream-wetland interactions;
APPENDIX D: CVPIA TITLE 34 OF PUBLIC LAW 102-  

(4) measures needed to restore anadromous 

fisheries to optimum and sustainable levels in 

accordance with the restored carrying capacities 

of Central Valley rivers, streams, and riparian 

habitats;

(5) development and use of base flows and channel 

maintenance flows to protect and restore natural 

channel and riparian habitat values;

(6) implementation of operational regimes at State 

and Federal facilities to increase springtime flow 

releases, retain additional floodwaters, and assist 

in restoring both upriver and downriver riparian 

habitats;

(7) measures designed to reach sustainable harvest 

levels of resident and anadromous fish, including 

development and use of systems of tradeable 

harvest rights;

(8) opportunities to protect and restore wetland and 

upland habitats throughout the Central Valley;

(9) measures to enhance the firm yield of existing 

Central Valley Project facilities, including 

improved management and operations, 

conjunctive use 

opportunities, development of offstream storage, 

levee setbacks, and riparian restoration.”

Use of Project Facilities for Water 

Banking Section 3408 (d) 

“The Secretary, in consultation with the State of 

California, is authorized to enter into agreements 

to allow project contracting entities to use project 

facilities, where such facilities are not otherwise 

committee or required to fulfill project purposes 

or other Federal obligations, for supplying carryover storage of irrigation and other water for 

drought protection, multiple-benefit credit-storage 

operations, and other purposes. The use of such 

water shall be consistent with and subject to State 

law. All or a portion of the water provided for 

fish and wildlife under this title may be banked for 

fish and wildlife purposes in accordance with this 

subsection.”

Land Retirement – Section 3408 (h)

“The Secretary is authorized to purchase from willing 

sellers land and associated water rights and other 

property interests ... which receives Central Valley 

Project water under a contract executed with the 

United States, and to target such purchases to areas 

deemed most beneficial to the overall purchase 

program, including the purposes of this title.”