U.S. Department of the Interior

Bureau of Reclamation 

U.S. Fish and Wildlife Service July 2013

Central Valley Project 

Improvement Act

Public Law 102-575

Annual Report

Fiscal Year 2012
Cover photographs:

Top: Red Bluff Diversion Dam - Gates Up. Photo courtesy of USBR.

Center: Black-tailed Jackrabbit, San Luis National Wildlife Refuge. Photo courtesy of 

USFWS.

Bottom: Spawning Chinook salmon and juvenile steelhead on gravel placed in 2012 in 

Goodwin Canyon. Photo courtesy of USBR.
TABLE OF CONTENTS i

Central Valley Project Improvemen

Table of Contents
ii CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Table of Contents

EXECUTIVE SUMMARY.......................................................................................................................................ES-1

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

CHAPTER 2 - FISHERIES RESOURCE AREA........................................................................................................13

3406 (b)(1) Anadromous Fish Restoration Program............................................................................................14

3406 (b)(1) Bay-Delta Activities ...........................................................................................................................25

3406 (b)(1) “Other” & (b)(23) Trinity River Restoration Program .........................................................................26

3406 (b)(4) Tracy (Jones) Pumping Plant Program.............................................................................................30

3406 (b)(10) Red Bluff Diversion Dam.................................................................................................................32

3406 (b)(12) Clear Creek Restoration Program...................................................................................................35

3406 (b)(13) Spawning and Rearing Habitat Restoration Program.....................................................................39

3406 (b)(16) Comprehensive Assessment and Monitoring Program...................................................................42

3406 (b)(21) Anadromous Fish Screen Program.................................................................................................45

Public Law 111-11 San Joaquin River Restoration Program ...............................................................................47

3406 (g) Ecosystem and Water Systems Operations Models .............................................................................49

CHAPTER 3 - CVP WATER OPERATIONS RESOURCE AREA.............................................................................53

3406 (b)(2) Dedicated 800,000 acre-feet Project Yield........................................................................................54

3406 (b)(3) Water Acquisition Program – Instream Water...................................................................................57

3406 (b)(9) & (b)(19) Flow Fluctuations and Reservoir Storage..........................................................................59

3404 (c) & 3405 Contract Renewals and Water Transfers ..................................................................................61

CHAPTER 4 - REFUGES RESOURCE AREA .........................................................................................................63

3406 (d)(1), (2) & (5) Refuge Water Supply Program..........................................................................................64

3406 (d)(2) Refuge Water Acquisition..................................................................................................................67

3406 (d)(1), (2) & (5) Refuge Water Conveyance................................................................................................69

3406 (d)(5) Refuge Facilities Construction Component.......................................................................................72

CHAPTER 5 - OTHER RESOURCE AREA..............................................................................................................75

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

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

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS ..............................................82

APPENDICES ...........................................................................................................................................................87

Appendix A: Acronyms........................................................................................................................................88

Appendix B: Glossary of Terms ..........................................................................................................................89

Appendix C: CVPIA Title 34 of Public Law 102-575 ...........................................................................................92

Appendix D: Maps ..............................................................................................................................................96

LIST OF FIGURES

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

Figure ES-2: FY 2012 Financial Obligations By Action Category .................................................................ES-11

Figure ES-3: FY 2012 Financial Obligations By Fund Source......................................................................ES-11

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

Figure 2: Program Financial Obligations By Action Category to Date ..................................................................7

Figure 3: Program Financial Obligations By Fund Source to Date.......................................................................7

Figure 4: FY 2012 Financial Obligations By Action Category ...............................................................................8

Figure 5: FY 2012 Financial Obligations By Fund Source....................................................................................8
TABLE OF CONTENTS iii

LIST OF TABLES

Table ES-1: FY 2012 Breakdown of Funding Obligations by Program Activity ...........................................ES-10

Table 1: FY 2012 Breakdown of Funding Obligations by Program Activity ...................................................9

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

 Production by Species within Central Valley River and Streams, 1992-2011................................15

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

 Evaluations by Watershed, FY 1992-2012 ....................................................................................16

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

 (53 Structural, 75 Non-Structural) .................................................................................................17

Table 5: Average Natural Production Numbers in Each Watershed Compared to the AFRP 

 Doubling Goal Targets, 1992-2011 ................................................................................................18

Table 6: FY 2012 Salmonid Production, Natural vs. Hatchery1 ..................................................................27

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2012.............................................28

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2012 ...............................28

Table 9: Rehabilitation Site Construction Summary, 2005-2012 ................................................................29

Table 10: Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan Actions .........31

Table 11: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2012.................................41

Table 12: AFSP Projects by Watershed and Cubic Feet per Second (cfs) Screened, 1994-2012................46

Table 13: Ecosystem and Water System Operations Models Developed To Date........................................51

Table 14: Allocation Target and Use of (b)(2) Water, 2001-2012 ..................................................................55

Table 15: FY 2012 Use of (b)(2) Water by Location......................................................................................56

Table 16: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 1994-2012..........58

Table 17: Carryover Storage at Shasta and Trinity Reservoirs, 1998-2012..................................................60

Table 18: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2012.........................................................68

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

 2002-2012 .....................................................................................................................................70

Table 20: Water Targets and Deliveries for Each Refuge (FY 2012).............................................................71

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

Table 22: Acres of Habitat Protected and Restored by the (b)(1) “Other” Program, 1996-2012, 

 Using HRP Funds..........................................................................................................................77

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2012 ................................79

EXECUTIVE SUMMARY ES-

Central Valley Project Improvemen

Executive Summary
ES-2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

PURPOSE

This fiscal year (FY) 2012 CVPIA Annual

Accomplishments Report summarizes the actions 

authorized under the Central Valley Project 

Improvement Act (CVPIA or Act) of 1992 an

highlights FY 2012 accomplishments (October 1, 

2011 - September 30, 2012). 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, 2012 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). 

Chapter 6 shows the current Programs and their 

status toward completion of goals. Complete and 

inactive programs are listed along with a description 

of their status which includes programs that have been 

closed out and incorporated into other programs. The 

relevant Sections of the Act are provided for reference 

in Appendix C. 

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. 

2012 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 

Executive Summary

Ring-necked duck climbing up out of the water, Colusa NWR
EXECUTIVE SUMMARY ES-

type is determined by precipitation and is therefore 

indicative of local and regional conditions that 

influence climate, snowpack and runoff. 

Water Year (WY) 2012 was the driest since the 

2007-2009 drought. Near record dry conditions 

during the winter precipitation months were followed 

by an unseasonably wet late spring. The final Water 

Year 2012 classification was below-normal for the 

Sacramento Valley and dry for the San Joaquin 

Valley. Impacts of the dry year were somewhat

minimized due to the good carry-over storage from 

WY 2011.

CVPIA GOALS AND FY 2012 

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 2012 accomplishments. These 

summaries offer a snapshot of the work accomplished 

in FY 2012. Chapters 2, 3, 4 and 5 of this report 

provide more information on the accomplishments 

of each program, while a synopsis of the programs 

targets, status to date and 2012 accomplishments are 

presented in Chapter 6.

Two ongoing programs, Flow Standards and 

Objectives and Short Pulse Flows, are incorporated 

into the operations of overarching programs such as 

Clear 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. 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 estimates of natural production,

the CVPIA Program uses the suite of structural and

non-structural restoration actions from the Plan to 

measure progress. For example, on Clear Creek and 

the Trinity River, 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.

While the fisheries programs are currently 

administered individually, the Structured Decision 

Making process (formerly the Science Based 

Management Framework approach) discussed below 

under Recent Developments aims to coordinate, 

integrate and prioritize CVPIA efforts across

geographic areas. 

2012 Accomplishments

Anadromous Fish Restoration Program 

(AFRP), 3406 (b)(1)

Sacramento Basin

In 2012, the AFRP focused on actions within the

Sacramento and San Joaquin basins that will 

contribute to the natural production doubling goal. 

Within these basins, the actions occurred within 18 

watersheds. 2012 projects include channel and 

habitat restoration, fish passage, and operational 

flow management. Monitoring of projects, from preconstruction baseline conditions to post-construction 
ES-4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

performance analysis, occurred using techniques 

such as acoustic telemetry, rotary screw traps, snorkel 

surveys and aerial photography. 

In 2012, the program completed construction on

the following projects: Budiselich Flashboard Dam 

boulder weir retrofit, improving access to 8 miles 

of anadromous fish habitat; Hammon Bar riparian 

planting project, restoring 1.25 acres of riparian 

habitat; Wildcat Dam and Canal project, opening up 

42 miles of aquatic habitat; Antelope Creek Crossing 

Repair project, improving passage to 6.5 miles of 

spawning and holding habitat; American River at 

Lower Sailor Bar project, supplementing spawning 

habitat through the placement of 5,000 cubic yards of 

gravel; Merced River Floodplain project, enhancing 

spawning habitat through the placement of 20,000 

cubic yards of gravel; Mokelumne River Spawning 

Habitat Improvement project, injecting 3,500 tons of

spawning gravel; and the Honolulu Bar Floodplain 

Restoration project, restoring 2.47 acres of riparian 

floodplain, creating 0.7 acres of new floodplain, 

adding 12,500 cubic yards of spawning gravel and 

restoring 485 feet of side channel habitat.

In addition to construction projects, the program also

provided technical expertise for FERC proceedings 

for the Don Pedro Hyrdoelectric Project, Merced Falls 

and Merced River Hydroelectric Projects. 

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

P.L. 111-11 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)(1) San Joaquin River 

Restoration 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-

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

The program 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. 

Red Bluff Diversion Dam (RBDD), 3406 

(b)(10)

Construction of the new, 2,500-cfs permanent 

pumping plant and fish screen was substantially 

completed in 2012 with the installation of the pumps 

and motors, completion of the pumping station and 

fish screen contract and completion of the construction 

and planting phase of the Terrestrial Mitigation. The 

program also conducted green sturgeon sampling 

over a 94-river-kilometer range to determine 

spawning and larvae emergence timing. 

Clear Creek Restoration Program (CCRP), 

3406 (b)(12)

The Clear Creek Restoration program placed 10,000 

tons of gravel in four sites during 2012: Guardian 

Rock (aka belowNEED Camp), Placer Bridge, Clear 

Creek Road Crossing, and the Tule Backwater. The 

CCRP met its goal of providing base flows of 200 

cfs between October 1–May 31. In the spring of

2012, two pulse flows were provided to help attract 

spring-run Chinook to Clear Creek. The program 

also conducted three Environmental Water Program 

workshops which aim 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. 

Spawning and Rearing Habitat 

Restoration Program, 3406 (b)(13)

The program created or improved spawning habitat 

by placing 15,000 tons of gravel below the Keswick 

Dam on the Sacramento River, 3,000 tons of gravel 

at Goodwin Camp Float Tube Pool on the Stanislaus 

River, and 24,510 tons of gravel and created a 

400-foot side channel at lower Sailor Bar on the 

American River. Biological and physical conditions 

were monitored to evaluate the effectiveness of the 

completed gravel placement projects.

Gravel injection at Keswick Site
ES-6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Comprehensive Assessment and 

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

CAMP funded several salmon monitoring projects 

including constant fractional marking at Nimbus 

and Coleman Fish Hatcheries, video monitoring on 

Cottonwood and Cow Creeks, rotary screw traps at 

Caswell State Park on the Stanislaus River, and visual 

surveys on Battle Creek and the Sacramento River. 

The Program also created data management tools 

for the CVPIA including workplan data entry and

performance accomplishment spreadsheets.

Anadromous Fish Screen Program 

(AFSP), 3406 (b)(21)

The AFSP completed construction of the Bella Vista 

Fish Screen and removed an existing RD 108 South 

Steiner diversion on the Sacramento River, replacing it 

with pipeline facilities to convey irrigation water from 

an existing RD 108 Wilkins Slough Pumping Plant and 

Fish Screen. The Program continued construction on 

the Natomas Mutual Sankey Fish Screen project. The 

AFSP completed a three-year (2010-2012) hydraulics 

and fish behavioral study to identify critical factors 

resulting in fish losses at water diversions. 

Ecosystem and Water Systems Operation 

Models, 3406 (g)

The Models Program developed, modified and 

utilized the following models in support of 7 of the 

9 integral areas: CalSim II, CalLite, CalSim 3.0

HEC-5Q, C2VSim, ANN Model, DSM2, inSALMO, 

and HydroGeoSphere. The Program finalized 

development of CalLite 2.0 and made it publicly 

available from California Department of Water 

Resources (DWR) website. 

Trinity River Basin

Trinity River Restoration Program, 3406 

(b)(1) “Other” and (b)(23) 

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)

In 2012, the TRRP managed flows to facilitate

geomorphic processes, especially at newly 

constructed channel rehabilitation sites. Channel 

rehabilitation projects were implemented at Upper 

Junction City and Lower Steiner Flat sites. Five 

watershed projects including feasibility studies and 

project designs were completed in FY 2012 that kept 

approximately 30,000 CY of fine sediment out of 

the mainstem. The Program conducted monitoring 

and assessment of biological and physical conditions 

to determine project effectiveness and salmon 

production.

San Joaquin River Basin

San Joaquin River Restoration Program, 

P.L. 111-11 

The CVPIA includes a provision to authorize activities

for the San Joaquin River Restoration Program (SJRRP) 

under Section 3406 (c)(1) of the Act. On March 30, 

2009, Congress enacted Public Law 111-11, Section 

10007, Compliance with Central Valley Project 

Improvement Act. This law “finds and declares that

the San Joaquin River Restoration Settlement (SJRRP) 

Act (Settlement) satisfies and discharges all of the 

obligations” stipulated under CVPIA Section 3406

(c)(1). Restoration implementation activities, including 

planning and environmental studies now carried out 

under PL 111-11 aim to 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 and authorizes up to $2 million a 
EXECUTIVE SUMMARY ES-

year from the Central Valley Project Restoration Fund 

under the PL 111-11 to supplement the program’s 

funding under the Settlement.

In FY 2012, the SJRRP began a project to monitor and

control five riparian invasive species: red sesbania, 

salt cedar, giant reed, Chinese tallow, and sponge 

plant. The Program compiled the 2011 Annual 

Technical Report (ATR) in March 2012 and the 

Final 2012 MAP in November 2011. The Program 

also began modifying the Ecosystems Diagnosis 

and Treatment (EDT) modeling platform to support 

the continued development of the SJRRP Fisheries 

Management Plan. 

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; 

3406(b)(2) Dedicated Project Yield; 3406 (b)

(3) Water Acquisition Program; 3406 (b)(9)/(b)

(19), Flow Fluctuations and Reservoir Storage; and 

Section 3404 (c) and 3405, Contract Renewals 

and Water Transfers. 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.

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 2012. The program 

supported actions on the American, Sacramento and 

Stanislaus Rivers, Clear Creek, and at the CVP Jones 

Pumping Plant to augment base flows and provide 

pulse flows in support of fisheries, endangered 

species, and water quality requirements. 

Water Acquisition Program – Instream 

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

The Instream WAP acquired 25,714 AF in the Merced

River for the Lower San Joaquin River.

Flow Fluctuations (FFP) and Reservoir 

Storage (RSP), 3406 (b)(9) and (19)

The FFP, in partnership with the 3406 (b)(2) 

Dedicated Yield Program, surveyed salmon and 

steelhead redds on Clear Creek, the American 

River, and the Sacramento River and performed two 

salmonid isolation pool surveys on the American River. 

Additionally, a Flow Fluctuation Study was conducted 

on the Stanislaus River. The RSP met the carryover 

targets for Shasta and Trinity reservoirs with 2.592 

MAF and 1.800 MAF, respectively. 

Contract Renewals and Water Transfers, 

3404 (c) and 3405

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.

To date, 88 long term renewal contracts and 28 

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. 
ES-8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Reclamation approved the transfer of 524,036 

AF of CVP water in FY 2012. The majority of 

transfers stayed within current use from agricultural 

to agricultural and the second largest transfer 

classification was from agricultural to municipal and 

industrial use.

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 2013, 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. 

Water Acquisitions Program – Refuge 

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

In 2012, the RWAP purchased 47,263 AF of water

for Water Year 2012. The program also monitored 

the quality of the water after it is applied to refuges 

through the Real-time Water Quality Monitoring 

Project in the Grasslands Ecological Area. 

Refuge Water Conveyance Program 

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

The Program delivered an estimated 402,454 AF of 

Level 2 water and an estimated total of 55,515 AF 

of Incremental Level 4 water to the refuges during FY

2012. Of the Level 2 water sources, a total of 39,064 

AF was delivered from diverse, non-CVP sources. 

Refuge Facilities Construction 

Component (RFCP), 3406 (d)(5)

The RFCP provided operational repairs to the East 

Bear Creek Unit of the San Luis National Wildlife 

Refuge Complex (East Bear Creek) Pumping 

Plant. In conjunction with the RWCP, the RFCP

completed construction of the Gray Lodge and 

Pixley Groundwater Well Projects. The Program also 

completed the construction of four new groundwater 

production wells at the Grasslands Resource 

Conservation District. In addition, the final design of

the Biggs-West Gridley Water District (BWGWD) 

Facilities Improvement Project was completed and

when fully constructed, BWGWD will have sufficient 

conveyance capacity for Full Level 4 water deliveries 

to the Gray Lodge WA. 

Other Resources Area Goals

The fourth focus of the CVPIA restoration initiatives

is directed at terrestrial habitat and species; water 

quality and conservation. Provisions supporting this 

initiative include Section 3406 (b)(1) “other,” Habitat 

Restoration Program (HRP); and Section 3408 (h), 

Land Retirement Program (LRP). 

Habitat Restoration Program (HRP), 3406 

(b)(1) “Other”

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, and captive breeding. 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. 
EXECUTIVE SUMMARY ES-

In 2012, the HRP protected 520 acres of alkali scrub,

grassland, and riparian woodland habitats in Fresno 

County; 194 acres of alkali scrub and grassland 

habitats in Kern and San Luis Obispo counties; and 

198 acres of grassland habitat in Tulare County. 

The HRP also provided funds for a Metcalf Canyon 

jewelflower captive propagation and reintroduction 

project in southern Santa Clara County. 

Land Retirement Program (LRP), 3408 (h)

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.

In 2012, the LRP planted 9,500 pounds of locally

grown seed from native plants on 300 acres of 

previously acquired land at the Atwell Island site.

Through the removal of irrigation, the program 

reduced the amount of agricultural drainage water at 

the Atwell Island site by approximately 4,100 acrefeet in FY 2012.

FUNDING 

For FY 2012, $53.1 million was appropriated to the 

Restoration Fund. As shown in Figures ES-2 and ES-3, 

a total of $83.1 million was obligated on CVPIA

projects from a combination of funding sources: 

Restoration Funds ($48.0 million), Water and Related 

Resources ($22.2 million), ARRA funds ($1.3 million), 

state cost share funds ($1.9 million), and Bay-Delta 

funds ($9.6 million). See Table ES-1 for a breakdown 

of funding for each CVPIA Program activity in FY

2012.

In 2012, 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 Screen 

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 for FY 

2014. 

RECENT DEVELOPMENTS 

Refuges Independent Review

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 Independent Review

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 
ES-10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay Delta

Funds

ARRA

Funds Total Funds

3405(a) Water Transfer Program 0 0 0 94,348 0 94,348

3406(b)(1) Anadromous Fish Restoration Program 507,224 6,326,848 0 8,004,939 0 14,839,011

3406(b)(1) Habitat Restoration Program 0 1,485,765 0 0 0 1,485,765

3406(b)(1) Trinity River Restoration Program 7,672,904 2,990,009 0 0 0 10,662,914

3406(b)(2) Dedicated Project Yield 0 776,136 0 0 0 776,136

3406(b)(3) Water Acquisition 

Program - Instream Water

 175,000 1,983,287 0 0 0 2,158,287

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

Plant Program

Tracy (Jones) 

Pumping Plant1

 1,346,838 0 0 0 0 1,346,838

Two Gates 0 0 0 18 0 18

3406(b)(5) Contra Costa Pumping Plant No. 1 9,309 0 0 0 744,350 753,660

3406(b)(9) Flow Fluctuations 0 14,779 0 0 0 14,779

3406(b)(10) Red Bluff Diversion Dam 5,041,473 0 3,472 0 492,451 5,537,396

3406(b)(12) Clear Creek Restoration Program 32,020 986,495 0 0 0 1,018,514

3406(b)(13) Spawning Gravel 0 758,228 0 0 0 758,228

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 3,621,718 0 0 0 3,621,718

3406(b)(20) Glenn Colusa Irrigation District 294 0 0 0 0 294

3406(b)(21) Anadromous Fish Screen Program 4,300,000 6,013,716 1,914,337 1,500,000 0 13,728,053

3406(b)(23) Trinity River Restoration 2,974,468 0 0 166 0 2,974,633

PL 111-11 San Joaquin River Restoration Program 0 2,599,325 0 0 0 2,599,325

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

3406(d)(2)` Refuge Water Supply Level 4 0 6,662,257 0 0 0 6,662,257

3406(d)(5) Refuge Facilities 

Construction Program

Construction 76 493,849 0 0 89,746 583,671

Wheeling (32,901) 11,360,280 0 0 0 11,327,671

3406(d)(5) San Joaquin Basin Action Plan 138,073 130,323 0 0 0 268,397

3406(g) Ecosystem & Water System Operations 

Models

 0 554,129 0 0 0 554,129 

3408(h) Land Retirement Program 21,209 494,162 0 0 0 515,372

3410 CVPIA Administration (18,383) 794,243 0 0 0 775,860

TOTAL FUNDING OBLIGATED 22,167,605 48,045,549 1,917,809 9,599,471 1,326,547 83,056,981

1

 A negative amount represents a recovery of a prior year obligation.

Table ES-1: FY 2012 Breakdown of Funding Obligations by Program Activity
EXECUTIVE SUMMARY ES-1

Figure ES-2: FY 2012 Financial Obligations By Action Category

Figure ES-3: FY 2012 Financial Obligations By Fund Source
ES-12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

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 panel’s recommendations, the 

Department of the Interior (DOI) is developing a

improved science-based, structured 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, structured decision making 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 

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

In FY 2012, several key CVPIA activities contribute

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 3,000 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. 

Red Bluff Fish Passage

Construction of the new, 2,500-cfs permanent 

pumping plant and fish screen was substantially 

completed in 2012 and the dam gates were not 

operated in 2012. Fish passage for all species was 

unimpeded. 
EXECUTIVE SUMMARY ES-1

Two cock pheasants fighting for territory, Sacramento NWR.

INTRODUCTIO 

Central Valley Project Improvemen

Chapter 1

Introduction
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

PURPOSE

This fiscal year (FY) 2012 CVPIA Annual

Accomplishments Report summarizes the actions 

authorized under the Central Valley Project 

Improvement Act (CVPIA or Act) of 1992 an

highlights FY 2012 accomplishments (October 1, 

2011 - September 30, 2012). 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, 2012 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). 

Chapter 6 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

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 irrigation 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. 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 

Chapter 1 - Introduction
INTRODUCTIO 

Figure 1: Central Valley Project (CVP) System
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

is diverted along the way, with the remainder flowing 

into the Sacramento-San Joaquin River Delta, where 

CVP water co-mingles 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. 

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. In response, a new imperative for

resource management and ecological stewardship 

has evolved. 

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 four 

broad resource areas: Fisheries, Water Operations, 

Refuges and Other Terrestrial Resources. 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.

A synopsis of the programs targets, status to date and 

2012 accomplishments are presented in Chapter 6.

FUNDING

CVPIA fish, wildlife, and improved water management

and conservation actions are implemented through 

a variety of agreements 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 is reimbursable from project 

beneficiaries, a non-reimbursable federal expenditure, 

from the State; or a combination of these sources. The 

RF, established by Section 3407(a) 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 for mitigation and 

restoration payments specified in Section 3407(d)(2)

(A). The $30 million payment ceiling is calculated on 

a 3-year rolling average. In addition, 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

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

funds and the American Recovery and Reinvestment 

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

total of $1.5 billion has been obligated by the CVPIA

Program over the past 19 years, as shown in Figures 

2 and 3. 

FY 2012 

For FY 2012, $53.1 million was appropriated to the 

Restoration Fund. As shown in Figures 4 and 5, a total 

of $83.1 million was obligated on CVPIA projects

from a combination of funding sources: Restoration 

Funds ($48.0 million), Water and Related Resources 

($22.2 million), ARRA funds ($1.3 million), state cost 

share funds ($1.9 million), and Bay-Delta funds ($9.6 

million). See Table 1 for a breakdown of funding for 

each CVPIA Program activity in FY 2012

American Recovery and Reinvestment 

Act (ARRA) Funding

ARRA’s funding in FY 2012 enhanced the CVPIA

Program’s capabilities to restore fisheries and wildlife 

refuges. To date, approximately $152 million has 

been awarded to Reclamation for CVPIA Program

activities. In FY 2012, ARRA funds were obligated

for the following: Contra Costa Canal Pumping Plant 

Program, 3406 (b)(5), obligated $0.7 million to 

complete construction on the Contra Costa Canal fish 

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

(10), obligated $0.5 million to complete construction 

on the permanent pumping plant for the fish passage 

project, and $0.09 million was obligated for refuge 

groundwater wells. 

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 and extended SCAMPI for an

additional 3 years to December 31, 2014.

In 2012, 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 Screen 

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 for FY 

2014. 

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 
6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

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. 

Antelope Creek wildlife area crossing
INTRODUCTIO 

Figure 2: Program Financial Obligations By Action Category to Date

Figure 3: Program Financial Obligations By Fund Source to Date
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Figure 4: FY 2012 Financial Obligations By Action Category

Figure 5: FY 2012 Financial Obligations By Fund Source
INTRODUCTIO 

Table 1: FY 2012 Breakdown of Funding Obligations by Program Activity

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay Delta

Funds

ARRA

Funds Total Funds

3405(a) Water Transfer Program 0 0 0 94,348 0 94,348

3406(b)(1) Anadromous Fish Restoration Program 507,224 6,326,848 0 8,004,939 0 14,839,011

3406(b)(1) Habitat Restoration Program 0 1,485,765 0 0 0 1,485,765

3406(b)(1) Trinity River Restoration Program 7,672,904 2,990,009 0 0 0 10,662,914

3406(b)(2) Dedicated Project Yield 0 776,136 0 0 0 776,136

3406(b)(3) Water Acquisition 

Program - Instream Water

 175,000 1,983,287 0 0 0 2,158,287

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

Plant Program

Tracy (Jones) 

Pumping Plant1

 1,346,838 0 0 0 0 1,346,838

Two Gates 0 0 0 18 0 18

3406(b)(5) Contra Costa Pumping Plant No. 1 9,309 0 0 0 744,350 753,660

3406(b)(9) Flow Fluctuations 0 14,779 0 0 0 14,779

3406(b)(10) Red Bluff Diversion Dam 5,041,473 0 3,472 0 492,451 5,537,396

3406(b)(12) Clear Creek Restoration Program 32,020 986,495 0 0 0 1,018,514

3406(b)(13) Spawning Gravel 0 758,228 0 0 0 758,228

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 3,621,718 0 0 0 3,621,718

3406(b)(20) Glenn Colusa Irrigation District 294 0 0 0 0 294

3406(b)(21) Anadromous Fish Screen Program 4,300,000 6,013,716 1,914,337 1,500,000 0 13,728,053

3406(b)(23) Trinity River Restoration 2,974,468 0 0 166 0 2,974,633

PL 111-11 San Joaquin River Restoration Program 0 2,599,325 0 0 0 2,599,325

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

3406(d)(2)` Refuge Water Supply Level 4 0 6,662,257 0 0 0 6,662,257

3406(d)(5) Refuge Facilities 

Construction Program

Construction 76 493,849 0 0 89,746 583,671

Wheeling (32,901) 11,360,280 0 0 0 11,327,671

3406(d)(5) San Joaquin Basin Action Plan 138,073 130,323 0 0 0 268,397

3406(g) Ecosystem & Water System Operations 

Models

 0 554,129 0 0 0 554,129 

3408(h) Land Retirement Program 21,209 494,162 0 0 0 515,372

3410 CVPIA Administration (18,383) 794,243 0 0 0 775,860

TOTAL FUNDING OBLIGATED 22,167,605 48,045,549 1,917,809 9,599,471 1,326,547 83,056,981

1

 A negative amount represents a recovery of a prior year obligation.
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Refuges Independent Review

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 the reliability of Level 2 water 

deliveries improved since 2002. The report also found 

that 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 Independent Review

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 

Moonbow at Friant Dam
INTRODUCTIO  

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.

Specifically, the initial steps include developing the 

science-based, structured decision making 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 

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 (BO) analyzing the effects of the 

CVP and SWP operations on the threatened delta 

smelt and associated critical habitat. On June 4, 

2009, NMFS issued its BO analyzing the effects of 

the CVP and SWP operations on threatened and 

endangered (T&E) salmonids, green sturgeon, and 

killer whale and associated critical habitat. The 

consultation resulted in determinations of “likely to 

jeopardize the continued existence of listed species 

and likely to result in the destruction or adverse 

modification of critical habitat. The CVP and SWP 

are currently operating under the two BO’s, which set 

forth Reasonable and Prudent Alternatives (RPA’s) to 

avoid jeopardy to species and adverse modification 

of critical habitat during operation of the CVP and 

SWP. The BOs were both challenged in Federal 

District Court. The Court issued rulings on both BO’s 

requiring further analysis and reconsideration of 

specific RPA actions. In addition, the Court required

that Reclamation conduct a review in accordance 

with NEPA of the effects of the RPAs on the human 

environment. We are currently in the process of 

completing the review, and the court-mandated 

deadline is December 1, 2013.

In FY 2012, several key CVPIA activities contribute

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 3,000 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. 

Red Bluff Fish Passage

Construction of the new, 2,500-cfs permanent 

pumping plant and fish screen was substantially 

completed in 2012 and the dam gates were not 

operated in 2012. Fish passage for all species was 

unimpeded. 
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Bridge and Siphon under Red Bank Creek. Looking from upstream of Red Bank Creek
Central Valley Project Improvemen

Chapter 2

FISHERIES

RESOURCE 

AREA
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 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 (FRP) 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. The 22 rivers and streams are

specifically called out within Appendix B of the FRP 

and are listed in Appendix B of this report.

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. 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 o

eliminating entrainment of juveniles at diversions 

•	 Improve the opportunity for adult fish to reac

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 harves

and hatchery management 

•	 Involve partners in implementing and evaluatin

restoration actions

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 

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

such as fish screens or passage obstacles and nonstructural actions (75), such as flow fluctuations or 

studies (Table 4). 

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, 1992-2011

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

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 N/A N/A 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 N/A 6,392 385,842 1,047 505 7,720

1995 6,803 N/A N/A N/A 714,930 764 4,182 36,474

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

1997 2,591 N/A 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 N/A N/A N/A 403,023 17,243 5,439 11,130

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

2001 761 N/A 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 N/A N/A 528,336 9,106 10,882 13,269

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

2005 1,741 1,058,679 2,557 2,898 397,755 20,838 21,511 26,099

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

2007 551 252,275 1,530 10,559 107,253 30,509 4,142 13,138

2008 271 1,116,062 1,330 6,257 39,778 4,806 2,555 4,489

2009 624 830,641 10,272 6,258 30,604 4,350 4,070 2,492

2010 683 696,159 N/A N/A 102,821 5,577 1,552 2,064

2011 892 894,606 N/A N/A 170,273 5,669 897 3,687

Average

% of 

Goal

N/A

N/A

2,389

56%

 966,692

39%

2,948

147%

 6,237

 57%

360,465

48%

17,835

26%

 6,320

 5.7%

 13,654

 20%

 

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-

2011.

c Estimated abundance of adult striped bass in the Central Valley’s anadromous waters, 1992-2011. Estimates for 2007, 2008, 2009, 2010, and 

2011 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.
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Watershed

Total actions and 

evaluations in Final 

Restoration Plan

Actions and 

evaluations

completed to date

Actions and 

evaluations 

addressed in 

2012

% of actions 

and evaluations 

completed to date

American River 13 2 1 15

Antelope Creek 2 0 1 0

Battle Creek 12 8 3 67

Bear Creek 2 0 0

Bear River 8 0 1 0

Big Chico Creek 10 3 30

Butte Creek 39 32 82

Calaveras River 6 0 1 0

Central Valley-Wide 15 1 4 7

Clear Creek 7 5 71

Colusa Basin Drain 2 0 0

Cosumnes River 9 2 2 22

Cottonwood Creek 5 1 2 20

Cow Creek 4 0 2 0

Deer Creek 5 0 1 0

Elder Creek 2 0 0

Feather River 12 0 1 0

Merced River 8 0 4 0

Mill Creek 5 1 1 20

Miscellaneous Small 

Tributaries

 1 0 0

Mokelumne River 13 1 1 8

Ocean 3 0 0

Paynes Creek 2 0 0

Upper Mainstem 

Sacramento River

 22 8 2 36

Sacramento-San Joaquin 

Delta

 29 0 4 0

Mainstem San Joaquin 

River

 13 0 1 0

Stanislaus River 9 1 4 11

Stoney Creek 1 0 0

Thomes Creek 6 2 33

Tuolumne River 10 0 1 0

Yuba River 14 0 3 0

All Watersheds1 289 67 40 23

1

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

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

Evaluations by Watershed, FY 1992-2012
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

FY 2012 ACCOMPLISHMENTS 

The AFRP obligated $6,326,848 from the Restoration 

Fund and $507,224 from the Water and Related 

Resources Fund. 

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 2011. At the time this report 

was prepared, the 2012 data was not available.

The Central Valley Chinook salmon (all races) natural 

production average from 1992-2011 was 360,465 

fish which dropped below the 1967-1991 baseline 

average Chinook salmon production of 497,054 as 

a result of the continued low returns of fall run fish in 

2011 that totaled 170,273 fish (Table 2). Average 

Chinook salmon natural production for the period 

1992-2011 has exceeded the watershed doubling 

goal target on Clear, Butte, and Battle Creeks and 

in 2011 the Mokelumne River observed high returns 

(14,857 naturally produced fish) (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 five 

years (2007-2011). Spring-run numbers have trended 

upwards since 1991, but production was reduced 

in 2008 to 2011. Fall-run natural production has 

decreased to the baseline levels due to the recent 

stock collapse observed in 2007-2010 though 

numbers have increased in some watersheds in 2011. 

Late fall-run production had increased greatly since 

the low period (1993-1997) but continued to decline 

in 2011. 

Table 2 shows the yearly estimate of natural 

production for each anadromous fish species since 

1992 and Table 5 shows the average natural 

production estimate of Chinook salmon in each 

watershed from 1992-2011. Insufficient data are

available to estimate natural production of steelhead in 

the Central Valley. Monitoring data for white sturgeon 

and green sturgeon in San Pablo and Suisun bays are 

available for eleven years and ten years, respectively, 

between 1992 and 2009. The AFRP production target 

for 15-year-old white sturgeon was met once while the 

production target for green sturgeon >40 inches (total 

length) was met in 2001, 2005, 2006, and 2009. The 

Watershed 53 Structural Actions 75 Non-structural Actions

Number of structural 

actions completed 

in FY 2012*

Number of structural 

actions completed 

since 1992

Number of 

non-structural actions 

completed in 

FY 2012*

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 structural or non-structural actions were not completed in FY 2012, work continued on 20 watersheds 

throughout the Central Valley.

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

(53 Structural, 75 Non-Structural) 
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Watershed Species Doubling Goal Target

1992-2011 Average 

Natural Production 

Numbers Percent of Target

American River* Fall-Run 160,000 106,915 66.8

Antelope Creek Fall-Run 720 0 0

Battle Creek* Fall-Run 10,000 17,511 175.0

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 2,334 155.6

Clear Creek Fall-Run 7,100 10,685 150.0

Cosumnes River Fall-Run 3,300 737 22.3

Cottonwood Creek Fall-Run 5,900 1,687 28.6

Cow Creek Fall-Run 4,600 1,849 40.2

Deer Creek Fall-Run 1,500 838 55.8

Feather River* Fall-Run 170,000 88,563 52.1

Merced River* Fall-Run 18,000 6,637 36.9

Mill Creek Fall-Run 4,200 1,880 45.0

Miscellaneous Creeks Fall-Run 1,100 78 7.1

Mokelumne River* Fall-Run 9,300 8,372 90.0

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

Sacramento River Fall-Run 230,000 72,595 31.6

Stanislaus River Fall-Run 22,000 5,158 23.4

Tuolumne River Fall-Run 38,000 6,909 18.2

Yuba River Fall-Run 66,000 31,906 48.3

Central Valley Wide Fall-Run 750,000 398,273 53.1

Battle Creek* Late-fall-Run 550 684 124.0

Sacramento River Late-fall-Run 68,000 18,054 26.5

Central Valley Wide Late-fall-Run 68,000 17,835 26.2

Butte Creek Spring-Run 2,000 9,713 485.6

Deer Creek Spring-Run 6,500 2,024 31.1

Mill Creek Spring-Run 4,400 1,199 27.2

Sacramento River Spring-Run 59,000 718 1.2

Central Valley Wide Spring-Run 68,000 13,654 20.0

Calaveras River Winter-Run 2,200 0 0

Sacramento River* Winter-Run 110,000 6,320 5.7

Central Valley Wide Winter-Run 110,000 6,320 5.7

TOTAL All races 990,000 360,465 40.2

* Watersheds that contain a fish hatchery.

Table 5: Average Natural Production Numbers in Each Watershed Compared to the AFRP 

Doubling Goal Targets, 1992-2011
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

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 2011. The 2011 midwater trawl index for 

this species (892) increased slightly from 2009 (624), 

but the 2011 index was markedly below the 1967-

1991 baseline average of 2,129 shad and the AFRP 

production target of 4,300 shad. Monitoring of legalsize striped bass in the Central Valley’s anadromous 

waters has occurred in 15 out of 20 years between 

1992 and 2011 and the AFRP production target has 

not been met. 

About 23% of all Restoration Plan actions and 

evaluations (289) have been completed in the 1992 

to 2012 time period (Table 3). Of the 128 time certain 

high and medium priority actions, forty-six (46%) have 

been completed since 1992 (Table 4). Although nonstructural actions were not completed in FY2012, work 

continued on 20 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 - A structured decision making 

(SDM) prototype model was developed to assist in 

selecting the best actions for restoration given existing 

conditions, e.g., spawning versus rearing habitat. The 

model currently is being refined. Additional spawning 

and side channel habitat was restored in FY2012 

with the addition of 5,000 cubic yards of gravel. 

This project is co-implemented with the 3406(b)(13) 

program, U.S. Fish and Wildlife Service (USFWS), 

U.S. Army Corps of Engineers (ACOE), California 

Department of Fish and Wildlife (CDFW), and the 

Sacramento Area Water Forum.

Antelope Creek – The Juvenile Fish Passage 

Improvement Project at Edwards Diversion Dam

(Central Valley Evaluation 11) will prevent outmigrating salmonids from becoming entrained in 

the two diversion canals. In FY2012, the Tehama

County Resource Conservation District completed 

an alternatives analysis for juvenile fish passage. 

The Technical Advisory Committee has met with the 

diverters to determine the most feasible alternative. 

Design is expected to begin in FY2013. 

The Antelope Creek Crossing Repair Project at the 

Tehama Wildlife Area removed a road crossing 

that was a barrier to steelhead, spring-run Chinook 

Salmon, and fall-run Chinook salmon during dry 

years (Central Valley Evaluation 11). Construction was 

completed in 2012. This project improved passage to 

6.5 miles of spawning and holding habitat. This project 

was a cooperative effort between the USFWS and 

CDFW.

A draft report on the Lower Antelope Creek 

Geomorphic Analysis in Tehama County was 

completed in 2012 (Evaluation 1). Additional funding 

was also secured in FY2012 to collect data gaps that 

were identified in the draft report. The modification to 

the agreement was finalized in August 2012 and work 

will begin in the fall of 2012 on the new tasks. This is 

a cooperative project between the USFWS, CDFW, 

Los Molinos Mutual Water Company, NMFS, and the 

Tehama County Resource Conservation District. 

Battle Creek – The Battle Creek Salmon 

and Steelhead Restoration Project will restore 

approximately 42 miles of habitat in Battle Creek 

and an additional 6 miles of habitat in its tributaries.

Of the nine Bureau of Reclamation (USBR) contracts 

that constitute Phase 1A and 1B, seven have been 

awarded. At the Wildcat Dam & Canal site, both the 

dam & canal have been removed and the associated 

road repair is completed. A new fish screen and 

bypass is in place at Eagle Canyon Dam (Actions 2, 6, 

and 7). This project is a cooperative effort among the 

U.S. Department of Interior, USBR, USFWS, NMFS,

CDFW, and the Pacific Gas and Electric Company 

(PG&E).

Bear River – AFRP collected additional temperature 

data in 2012 in the Spenceville Wildlife Area 

in Dry Creek, a tributary to the Bear River. Also, 

reconnaissance level habitat assessments and snorkel 

surveys were implemented farther upstream. Habitat 

restoration targeting fall-run Chinook salmon which 

typically do not over-summer may be warranted. 

Cottonwood Creek – Post-construction topographical 

surveys of the Anderson-Cottonwood Irrigation District

(ACID) Siphon Project area in Cottonwood Creek
20 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

(Action 2) were completed in 2012. This project 

improved access to 30 miles of spawning habitat for 

fall- and spring run Chinook salmon and Central Valley 

steelhead. 

Additional data collection for the Cottonwood 

Creek Sediment Budget Project (Phase 1) including 

longitudinal and cross sectional profiles and turbidity 

testing occurred in FY2012. The USFWS also 

identified and established index sites to track changes 

in anadromous fish habitat over time. The USFWS 

also completed fish passage surveys on the South 

Fork and North Forks of Cottonwood Creek in 2012 

and identified the uppermost natural barriers within 

the two tributaries. The field study also documented 

spring-run Chinook salmon holding in the North Fork, 

where they were not known to occur. A final report 

on the sediment budget project is anticipated to be 

completed in 2013.

The National Environmental Policy Act (NEPA) 

environmental permitting on the Nonnative Invasive

Plant Management and Control Project (Action 5) 

was completed in August 2012. The initial treatment 

to remove nonnative invasive plants in Cottonwood 

Creek began in September 2012. This project is a 

cooperative effort between the USFWS, California 

Conservation Corps, CDFW, the Cottonwood Creek 

Watershed Group, and the Tehama County Resource 

Conservation District.

In 2012, the Alternatives Analysis (Phase 1) for

the South Fork Cottonwood Creek fish passage 

improvement project was initiated (Central Valley 

Evaluation 11). Reconnaissance surveys upstream of 

the Hammer diversion and hydropower dam were 

completed this year documenting excellent habitat 

for anadromous fish, therefore, justifying the need 

to improve fish passage at this site. A technical team 

representing the USFWS, CDFW, USBR, NMFS, 

and the landowner were convened to review the fish 

passage alternatives with the contractor. 

Cow Creek – The initial designs were completed 

in FY12 for the Clover Creek Fish Passage/Millville 

Diversion Dam Restoration Project. Fifty percent 

designs and the environmental compliance documents 

will be completed by spring 2013. This project will 

open up 10 miles of historic habitat to fall-run Chinook 

salmon and steelhead (Action 3). This is a cooperative 

project with the USFWS, CDFW, and the California 

Department of Water Resources (CDWR), the Natural 

Resources Conservation Service, and the Millville 

Ditch Association. 

A riparian habitat assessment was initiated in 2012 to 

determine riparian restoration priorities (Action 4) in 

Cow Creek. Aerial photos and site surveys are being 

used to inventory plant species, understory growth, 

and other riparian habitat parameters. This is a 

cooperative project with the USFWS, CDFW, and the 

Cow Creek Watershed Group. 

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 

fish passage and screening issues related to manmade barriers and diversions. A public meeting was 

held in 2012 to inform landowners of the project and 

surveys have begun in some parts of the creek. This is 

a cooperative project with the USFWS, CDFW, Cow 

Creek Watershed Group, and the Western Shasta 

Resource Conservation District.

Deer Creek – The agreement was finalized for the 

Lower Deer Creek Falls Fish Passage Improvement

Project (Phase 1) to assess the current ladder and 

develop engineered plans to repair or replace the 

Lower Deer Creek Falls fish ladder (Central Valley 

Evaluation 11). This project is a cooperative effort 

between the USFWS and CDFW.

An Interagency Agreement was established to set

up a network of acoustic receivers in the Deer and 

Mill Creek tributaries to the Sacramento River and 

implement a study that will assess reach specific 

survival rates of juvenile Chinook salmon from the 

Upper Sacramento River to the Delta. This study is 

being co-implemented by the USFWS, NMFS, the 

CDFW Ecosystem Restoration Program, and UC Santa 

Cruz. 

Feather River – Monitoring activities targeting North 

American green sturgeon, which is listed as threatened 

under the Endangered Species Act, continued in the 
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

Feather and Yuba rivers in FY2012. 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 – The Mill Creek fish passage assessment 

and restoration project was funded in FY2011 

(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. The three structures were surveyed in 2012 

and a draft alternatives report was submitted to the 

Technical Advisory Committee for review. This is a 

cooperative project between the USFWS, CDFW, Los 

Molinos Mutual Water Company, and the Mill Creek 

Conservancy.

A riparian habitat assessment was initiated in 2012 to 

determine riparian restoration priorities (Action 4) in 

Mill Creek. Aerial photos and site surveys are being 

used to inventory plant species, over story growth, and 

other riparian habitat parameters. This is a cooperative 

project with the USFWS, CDFW, and the Mill Creek 

Conservancy. 

Sacramento River – Redd stranding surveys were 

implemented between October 2011 and March 

2012 in the upper mainstem Sacramento River. 

Eighty-three redds were surveyed of which 25 were 

identified in areas of “concern” due to being so close 

to being dewatered and/or completely dewatered. 

Maintaining stable flows during egg incubation and 

emergence are important to reduce negative impacts 

to fall run and late-fall run Chinook salmon and 

steelhead fry production on the mainstem Sacramento 

River. This project is a cooperative effort between the 

USFWS, CDFW, CDWR, and Pacific States Marine 

Fisheries Commission with support from NMFS and 

Nor-Cal Fishing Guides and Sportsmen’s Association.

Yuba River – Cottonwood and willow pole cuttings 

were planted on 1.25 acres on Hammon Bar in 

FY2012. Overall plant survival after 9 months was 

87%. An additional 3.75 acres is scheduled for 

planting in FY2013. The planting area is intended 

to flood periodically under moderate flows and thus 

provide juvenile salmonids with improved rearing 

habitat. The cuttings also captured fine sediment and 

woody material during inundation in March 2012 thus 

enhancing floodplain processes at the site (Evaluation 

4). This project is a cooperative effort between the 

USFWS, CDFW, Bureau of Land Management (BLM), 

and the South Yuba River Citizens League. 

Vaki Riverwatcher systems continue to be operated on 

the north and south fish ladders at Daguerre Point Dam 

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. 

Reports assessing the 2011 data were presented at 

the Lower Yuba River Accord Symposium on July 9th, 

2012. AFRP staff continued to be an active participant 

on the Yuba River Management Team providing 

technical expertise on anadromous fish population 

monitoring. This project is a collaborative effort 

between the USFWS, NMFS, ACOE, CDFW, Yuba 

County Water Agency, and the Pacific States Marine 

Fisheries Commission. 

Accomplishments in the San Joaquin 

Basin

Calaveras River – The Budiselich Flashboard Dam 

boulder weir retrofit was completed this fiscal year 

on October 2011. This project restored access to 

about 8 miles of habitat (Action 3). Final designs were 

completed for the Caprini Low Flow crossing and 

the California Central Traction Railroad bridge sites. 

Permitting for these two sites is nearly finalized and 

both sites are expected to be implemented in summer 

2013. This project is a cooperative effort between the 

USFWS, CDFW, CDWR, Stockton East Water District, 

Fisheries Foundation of California, and the University 

of the Pacific. 

Cosumnes River – Post-project monitoring for the 

Cosumnes River Passage Improvement Project was

continued in 2012. Although the Cosumnes River 

did not connect in time for returning adult Chinook 

salmon to enter the system, the Fishery Foundation 

of California monitored the site during 2012 and 

reported that the site withstood substantially high flows 
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

encountered during spring 2012 and was performing 

well above design standards for physical stability and 

fish passage parameters. This project improved fish 

passage at Rooney Dam and restored access to about 

10 miles of habitat (Evaluation 2). 

The final designs to re-connect three historic tidal 

sloughs and restore 85 acres of floodplain habitat in 

the Delta within the Cosumnes River Preserve were 

completed (Delta Evaluations 4 and 6). Additional 

habitat assessments specifically targeting aquatic and 

terrestrial habitats and species were also completed in 

2012. This project is a cooperative effort between the 

USFWS, Ducks Unlimited, ACOE, and BLM.

Merced River – AFRP staff developed a new 

agreement for rotary screw trap monitoring of 

outmigrant juvenile salmon. This project documented 

the number of juvenile salmon and steelhead that 

outmigrated from the Merced River in 2012. Estimates 

of juvenile salmonid production were calculated and 

the existing outmigration database was updated. A 

fish health and condition study on juvenile Chinook 

salmon from the Merced River was also implemented 

to evaluate temperature effects and the incidence of 

Proliferative Kidney Disease (PKD) from March to May 

2012. Additional data to assess effectiveness of flow 

management and habitat restoration projects was 

collected. 

Outreach, planning, designs, and permitting for the 

Merced River floodplain and channel restoration 

project at Snelling (Action 3) was initiated in 2012. 

Preliminary designs for channel improvements, 

including improvements to benefit operations and 

maintenance to an existing diversion within the 

project footprint were completed. The environmental 

compliance and permitting was initiated with the 

completion of a Draft Environmental Assessment/Initial

Study and submission of environmental documents to 

meet requirements under Section 404 of the Clean 

Water Act and Section 106 of the National Historic 

Preservation Act. Pre-project monitoring which 

included a cultural resource assessment, vegetation 

surveys, nesting raptor survey, channel velocity and 

depth profiles, channel bathymetry and floodplain 

topographic surveys, benthic macro-invertebrate 

sampling, fish population monitoring, and substrate 

quality assessments were also completed for the 

Merced River floodplain and channel restoration 

projects this year. 

The second year of construction activities on the 

Merced River Ranch Project was completed on 

October 2011 where approximately 87,222 cubic 

yards of material were excavated and sorted to restore 

the floodplain and channel. An estimated 19,746 

cubic yards of gravel were placed in the Merced 

River to enhance spawning habitat. Additionally, 

one front-end loader spent eight workdays removing 

material from the head of the south bank side-channel. 

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. This project is a cooperative effort between 

the USFWS, CDFW, Merced County, and the Merced 

Irrigation District

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 FY2012. Staff 

provided study proposals and provided detailed 

comments on study plans for channel armoring, IFI

habitat modeling, temperature models, water balance 

operations models, and egg viability. AFRP is actively 

participating in the Merced River Technical Advisory 

Committee and developing ongoing partnerships with 

numerous stakeholders in the watershed. 

Mokelumne River – AFRP purchased and placed 

3,580 tons of spawning gravel for the Mokelumne 

River Spawning Habitat Improvement Project (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 FY2012, 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 (approximately 

90,000 acre feet) with Delta Cross Channel (DCC) 

operations in an effort to improve adult Chinook 

salmon returns (Delta Evaluation 5). In FY2012, the
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1  

FISHERIES

DCC gates were closed for 10 days in October 

2011. Preliminary results of this experiment found 

that straying of Mokelumne River origin fish can be 

reduced considerably and therefore contribute toward 

the watershed doubling goal for this river.

San Joaquin River – AFRP staff partnered with the 

CDFW to maintain VEMCOTM acoustic receivers in 

the San Joaquin River and continue an annual white 

sturgeon population assessment. AFRP experimented 

with egg mats to identify sturgeon spawning habitat. 

Consequently, 65 white sturgeon eggs were collected 

in 2012 at four sampling locations in the San Joaquin 

River, representing at least six spawning events and 

three new spawning locations. Additionally, 10 white 

sturgeon were captured and implanted with acoustic 

transmitters. Movements of these fish were tracked to 

learn more about the spatial and temporal distribution 

of white sturgeon in the San Joaquin River. Also, the 

AFRP partnered with USGS to map habitat-related 

physical characteristics along the San Joaquin River 

with a multibeam sonar, acoustic Doppler current 

profiler, and RTK-GPS. Physical habitat mapping 

efforts were focused on areas where white sturgeon 

adults and eggs were collected to refine our 

understanding of habitat preferences of this important 

species.

Stanislaus River – FY 2012 accomplishments 

included the collection of both juvenile and adult 

passage data via rotary screw trapping (juveniles) and 

a fish counting weir (adults) operated in partnership 

with Tri-Dam. A Chinook salmon juvenile acoustic 

study was completed this year. Preliminary results 

documented an estimated 7% (SE ± 3%) survival of 

juvenile Chinook salmon through the lower reaches of 

the Stanislaus River. AFRP also partnered with CDFW 

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 Lancaster Road Floodplain and Side-channel 

Restoration Project was completed and restored 640 

feet of riparian side channel habitat. Substantial postproject assessments were conducted at the Lancaster 

Road project site, including both physical and 

biological monitoring to evaluate project effectiveness. 

The Honolulu Bar Floodplain Restoration Project 

restored 2.47 acres of riparian floodplain, created 0.7 

acres of new floodplain, added 12,500 cubic yards 

of clean spawning gravel to the river, and restored 

485 feet of side-channel habitat. These projects were 

designed to increase juvenile salmonid rearing habitat 

and decrease predation (Action 2). The Stanislaus 

River floodplain restoration projects were implemented 

in partnership with ACOE, Oakdale Irrigation District,

Cramer Fish Sciences, FishBio, and CDFW. 

The Third Annual Stanislaus River Salmon Festival was 

held on November 5th, 2011 at the Knights Ferry 

Recreation Area, with AFRP staff heavily involved 

in organization and implementation of the event. 

The East Stanislaus Resource Conservation District, 

Modesto Junior College, Great Valley Museum, 

FishBio, U.S. Army Corps of Engineers, and both 

Oakdale and Knights Ferry schools played key roles in 

organizing the event.

Tuolumne River – Post-project monitoring at the 

Bobcat Flat Restoration Project collected fish through 

snorkel and seine surveys and benthic macroinvertebrate sampling in the constructed floodplain 

and side-channel in the Tuolumne River (Action 2). 

The Bobcat Flat Restoration Project restored 8 

acres of highly disturbed floodplain and about 1.6 

miles of fall run Chinook salmon and Central Valley 

steelhead spawning and rearing habitat. This project 

was a collaborative effort between USFWS, CDFW 

Ecosystem Restoration Program, and Friends of the 

Tuolumne River.

The AFRP continued to participate in the FERC 

proceedings for the Don Pedro Hydroelectric Project 

(P-2299) (Actions 1 and 6; Evaluations 1, 2, 3, and 4). 

AFRP participated in multiple relicensing meetings in 

FY2012. Staff provided study proposals and provided 

detailed comments on study plans for IFIM habita

modeling, temperature modeling, water balance 

operations modeling, O. mykiss age and growth, 

and juvenile Chinook salmon and predator acoustic 

telemetry studies. AFRP is collaborating with numerous 

stakeholders in the watershed through the relicensing 

process to develop conceptual models and evaluate 

the limiting factors and fishery resources in the 

Tuolumne River.
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Honolulu Bar Side Channel before (top) and after (bottom).
BAY-DELTA ACTIVITIES 3406 (b)(  

FISHERIES

Reclamation’s Bay-Delta Office (BDO) coordinates 

with the CVPIA office to respond to the urgent needs

of species in the Bay-Delta. As such, projects typically 

include those which address CVP operations and the 

Reasonable and Prudent Alternatives (RPA) prescribed 

by the regulating agencies. 

FY 2012 ACCOMPLISHMENTS

The BDO obligated $8,004,939 from the Bay-Delta 

Fund in FY12. 

BDO carried out several projects to benefit fish 

through the CVPIA. A network of about 30 tidal flow

and continuous water quality monitoring stations 

were maintained throughout the Delta to measure fish 

habitat quality, to inform hydrodynamic and sediment 

modeling efforts, and to provide CVP/SWP operators 

with an early warning system for the arrival of turbidity 

plumes containing delta smelt. These data are posted 

in near-real time on the US Geological Survey NWIS

web site. The BDO program also funded the ‘first flush’ 

study which focuses on the relationship between tidal 

flow and turbidity during the first high flow event of the 

winter. Two years of field data have been collected, 

one article has been published, and a second 

manuscript is in preparation. 

The BDO also funded (1) a six-year study of juvenile 

steelhead survival in the south Delta (required under 

the NMFS Biological Opinion); (2) a NMFS study of 

the genetic impacts of hatcheries on wild stocks; (3) a 

NMFS study on how large intake structures affect 

predators and predation on juvenile salmonids; (4) the 

first phase of a Chinook salmon life cycle model for 

use in Bay Delta Conservation Plan and other impact 

analyses and planning studies; and (5) the analysis of 

salmon movement past the Delta Cross Channel and 

Georgiana Slough using hydroacoustically tagged 

hatchery salmon smolts.

Bay-Delta Activities

 3406 (b)(1)

Non-physical barrier at Head of Old River
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

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 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 

as well as flow releases and sediment transportation 

that 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. 

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 tons (7000 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 

Trinity River Restoration 

Program

 3406 (b)(1) “Other” & (b)(23)
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “Other” & (b)(  

FISHERIES

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 2012 ACCOMPLISHMENTS 

In FY 2012, the Trinity River Restoration Program

obligated $2,974,468 from the Water & Related 

Resources Fund (b)(23), $7,672,904 from the Water & 

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

Funds of $2,990,009. 

Flows – Water Year 2012 was a Normal Water Year. 

Water temperature, channel rehabilitation construction, 

and riparian vegetation issues were considered in flow 

scheduling.

Water volume peak flow was modified to a 6,050 cfs 

release to facilitate geomorphic processes, especially 

at newly constructed channel rehabilitation sites. 

The ROD prescribed flow for a normal water year is 

647,000 AF.

Course Gravel and Channel Rehabilitation – 

Channel rehabilitation projects were implemented 

at Upper Junction City and Lower Steiner Flat sites, 

encompassing 4 of the 47 sites included in the 

ROD. Stakeholder concerns about pool fill and 

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

2011 16,071 5,757 7,026 1,379 27,518 5,349 14,390 4,707

2012 52,687 17,730 14,666 7,939 17,461 6,712 5,737 7,356

Average 16,110 6,079 4,851 2,145 19,175 8,918 12,347 11,566

 

1

 Data compiled by California Department of Fish and Game. Means are from 1992 to 2012 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. Trinity River Basin estimate for 2001 - 2012 (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 2012 Salmonid Production, Natural vs. Hatchery1
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2012

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

2012 Normal 647,000 AF 647,000 AF 6,080

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

scour affecting adult salmonid habitat and Program 

technical experts recommendations led to no coarse 

sediment (gravel) being added to the river in 2012. 

The program also continued planning and engineering 

designs for the next four channel rehabilitation 

projects. 

Five watershed projects including feasibility studies 

and project designs were completed in FY 2012 that 

kept approximately 30,000 CY of fine sediment out of 

the mainstem.

Monitoring and Assessment – approximately 

$5 million was obligated in FY 2012 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. Other results are included in the 

TRRP performance measures documents mentioned 

above as well as in reports located on the TRRP Online 

Data Portal (http://odp.trrp.net/).

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2012

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 2,30012,300

Lewiston-Dark Gulch 10,000

2009 High Flow Injections 2,300 8,000

Sawmill 5,700

2010 High Flow Injections 3,10013,500

Lowden Ranch Area and Reading Creek 10,400

2011 High Flow Injections 5,300 5,300

2012 Upper Junction City 0 0

Lower Steiner Flat 0

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.
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “Other” & (b)(  

FISHERIES

Table 9: Rehabilitation Site Construction Summary, 2005-2012 

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

2012 Upper Junction City, 

Upper Steiner Flat

 4 63,900 400 1.2 45

Total 28 710,950 1,660 13.90 252

* The No-Action alternative was chosen for the Steel Bridge Day Use Project Site.
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 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 10.

FY 2012 ACCOMPLISHMENTS 

The program obligated $1,346,838 from Water & 

Related Resources fund for the Tracy Fish Collection 

Facility, with no funds contributed from the Restoration 

Fund.

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. 

Replacement of the secondary louvers (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. This year we completed 

the NEPA and ESA documentation and drafted the 

NOAA fisheries variance. Engineering was on track 

this year. Design was completed to the 90% level and 

ready to be incorporated into a bid package. Funding 

is short; therefore we will likely be delayed for a year 

(to 2015). Continued assessments and search of land 

records 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 10: Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan 

Actions
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 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 created a seasonal lake in a wide portion 

of the Sacramento River, attracting both wildlife and 

recreational users. 

Operation of the dam impaired the ability of 

Chinook salmon and green sturgeon 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 winterrun 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. 

The NMFS’ 1993 BO on operation of the CVP/SWP 

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 

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). Central 

Valley spring-run Chinook salmon were listed under 

the Endangered Species Act in 1999. Operation of the 

RBDD gates also impaired the spawning migration of 

spring-run, and additional gates-in period adjustments 

were made. In 2006, green sturgeon that spawn

in the Sacramento River were listed as threatened 

under the Endangered Species Act. The RBDD gates 

prevented green sturgeon from migrating above the 

dam to spawn, and a new BO addressing operation 

of the CVP/SWP was completed in 2009. The 2009 

BO acknowledged that a new pumping facility was 

planned to replace the function of the RBDD.

Two temporary pumping plants allowed the gates to 

remain open for 101⁄2 months in 2011 (September 

– June 15). As a result of the 2009 BO, the gates 

are required to be raised year-round after 2011. The 

Red Bluff Diversion Dam

 3406 (b)(10)

Red Bluff Diversion Dam – Gates Up

Aerial view of Red Bluff Diversion Dam and completed 

pumping plant and fish screen (looking upstream)
RED BLUFF DIVERSION DAM 3406 (b)(10  

FISHERIES

temporary pumping plants did not meet the capacity 

needs to deliver year-round irrigation supplies to local 

farmers. The new pumping plant was substantially 

completed in 2012. Over the next several years the 

fish screen will be hydraulically and biologically 

evaluated. Completion of the new pumping plant 

allows the RBDD gates to remain open year-round 

without affecting deliveries to water contractors and 

the Sacramento Wildlife Refuge (SNWR).

PERFORMANCE MEASURES

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

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

Chinook salmon run that continued to be significantly 

blocked. The RBP aim was to achieve this target while 

maintaining water deliveries. Successful fish passage 

is now ensured, as the dam gates are no longer 

operated.

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

targeted while maintaining water deliveries to SNWR 

and other water contractors. Successful green sturgeon 

passage is now ensured now that the dam gates are 

no longer operated. 

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 provides a backup 

to conveyance via GCID’s facilities

FY 2012 ACCOMPLISHMENTS 

In FY 2012, the RBP obligated funding from a variety

of sources: 

•	$5,041,473 from Water and Related Resources 

Fund

•	$492,451 from the American Recovery & 

Reinvestment Act Fund

•	$3,472 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 was substantially 

completed in 2012: 

•	Moving Water Industries (MWI), Inc. h

installed the pumps and motors. 

•	Balfour-Beatty, Inc. completed the pumping

station and fish screen contract. 

•	Tehama Environmental Solutions completed 

the construction and planting phase of the 

Terrestrial Mitigation contract during calendar 

year 2012 and has begun the five year plant 

establishment phase.

Fish Passage - The dam gates were not operated in 

2012 and fish passage for all species was unimpeded. 

Compliance with 2009 NMFS BO – The RBP 

continued green sturgeon studies, in compliance with 

the BO-required actions. In 2012, sampling occurred

over a 94-river-kilometer range. Preliminary results 

indicate that green sturgeon spawning occurred from 

late April to late May, and larvae emerged from the 

spawning grounds between May and June.

Completed Pumping Plant and Fish Screen – August 2012
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Pumping plant complete in 2012. Looking from downstream to upstream
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 3

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. 

Section (b)(12) calls for 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 springrun 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 and upstream spawning. 

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 at that time, the 

necessity for further work would be subject to future 

needs. Since that time, the Clear Creek watershed 

has experienced two major wildfires, the Moon Fire 

in 2008 and the Dale Fire in July 2012. The CCRP 

is currently evaluating what measures are needed to 

address erosion concerns for the Dale Fire area.

Gravel Placement (Creation of Spawning 

Habitat) – The CCRP attempts to replenish Clear 

Creek spawning habitat areas with 25,000 tons of 

gravel every year. Clear Creek spawning gravel 

replenishment goal was erroneously reported in the 

Final CPAR, 2009 as 17,000 tons annually. This unit 

of measure should have been cubic yards. Applying 

a conversion factor, 17,000 cubic yards of spawning 

gravel equates approximately to 25,000 tons. This 

correction first occurred in the 2012 Accomplishment 

Report and therefore, the percentage of annual 

goal for this year forward will appear smaller than 

past years of the same amounts of gravel. 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 

Clear Creek Restoration 

Program

 3406 (b)(12)
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

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 various 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.

FY 2012 ACCOMPLISHMENTS 

In FY 2012, the CCRP obligated $986,495 from the

Restoration Fund and $32,020 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 2012 representing 40% of 

the annual target. Although more than 21,000 square 

feet of spawning habitat was created by the FY 2011 

gravel placement projects, the amount of habitat 

created by the 2012 injections cannot be determined 

until next year.

•	Gravel was placed in four sites during 2012: 

Guardian Rock (aka belowNEED Camp), Placer 

Bridge, Clear Creek Road Crossing, and the 

Tule Backwater.

The second annual evaluation of spawning gravel 

implementation and monitoring was submitted to 

NMFS as a requirement under the OCAP BO. As a 

result of studies in 2011 suggesting that gravel sizes 

specification should be modified in future years to 

improve use by spring Chinook, a new specification 

was developed and implemented for the 2012 

injections. The FWS and BOR, in coordination with 

the Clear Creek Technical Work Group will begin 

cooperatively and adaptively evaluate the efficacy of 

the new criteria in FY 2013.

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. Although the spring-run 

population numbers have been in decline, and (e.g.) 

the numbers of spring-run Chinook (7) were low in 

2011, the pulse flows are beneficial in attracting fish 

and promoting upstream movement. In the spring of

2012, two pulse flows were provided to help attract 

spring-run Chinook to Clear Creek. Pre- and post-flow 

event surveys conducted by FWS indicate that the 

pulse flows were successful in attracting adult fish; the 

data is currently under preparation. Similar flows will 

occur each year as directed by the NMFS OCAP BO.

Water temperature targets were partially met in 2011. 

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. The 2012 temperature 

data has not been fully analysed, however as of 

October 8, 2012, a total of 15 days exceeded 

temperature criteria, equating to meeting the target 

only 38% of the time.

In 2012, the juvenile salmonid flow habitat

relationships Instream Flow Incremental Methodolog

(IFIM) draft report was released for peer review

Work continued on bio-validation of the models. 

The resulting 14 IFIM flow-habitat models is bein

synthesized (integrated) as the “synthesis report” 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. This “synthesis report’ is currently 

in draft form.
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 3

FISHERIES

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. Three workshops were 

conducted during FY 2012.

Adaptive Management and Monitoring 

Spawning gravel-size specifications improved 

based on monitoring. Spawning ground surveys 

and spawning habitat suitability surveys identified 

that Chinook were no longer using the spawning 

gravel provided by the program in the reach directly 

downstream of Whiskeytown Dam. Gravel-size 

distributions suggested that only smaller size gravel 

was being delivered to spawning areas due to 

reduced high flows from Whiskeytown Reservoir, and 

that the size specifications being used for restoration 

in this area did not contain enough larger material. 

Therefore gravel size specifications were increased 

for projects implemented in 2012. Further monitoring 

will be needed to complete the adaptive management 

cycle and verify if Chinook use the new gravel. 

Spawning studies conducted by FWS and geomorphic 

studies conducted by GMA also indicated that some 

spawning gravel projects performed better than 

others. These results were used to improve projects 

conducted in 2012 and to prioritize sites for future 

spawning gravel augmentations. 

Stream channel restoration designs improved 

based on monitoring. In 2012, stream channel

restoration Phase 3B designs were improved by 

monitoring and evaluations. Based on monitoring 

results, plans and designs were made for habitat 

improvements in scour channels and riparian 

vegetation and for the reduction of negative habitat 

fragmentation by decommissioning of roads used 

during habitat restoration. Funding from the Ecosystem 

Restoration Program will allow completion of project 

construction. In addition, the final proposal for the

long term gravel supply project was greatly improved 

by the significant learning that has occurred in Clear 

Creek since 1996. This has included monitoring 

of birds, riparian vegetation, wetlands, mercury, 

and benthic macro-invertebrates in addition to 

geomorphology and fish.

Monitoring the impacts of wildfire will guide 

erosion control. The aforementioned 2008 wildfire in 

the South Fork Clear Creek tributary, and subsequent 

salvage logging and road building contributed 

to a significant instream sediment problem. These 

observations led to topographic surveys to quantify 

the amount of fine sediment delivered to the creek, 

bulk sampling to estimate changes in sediment size, 

and snorkel surveys to locate the downstream extent of 

sand deposition in pools. Information was synthesized

by the Clear Creek Technical Team to evaluate 

options and to identify the most appropriate solutions: 

sediment removal from a large pool, an erosion 

inventory, and erosion control. These actions may be 

funded in 2014. Funding will be needed to monitor 

and evaluate the effectiveness of these actions and 

to determine whether additional remedial measures 

will be necessary. Since the 2008 fires, the juvenile 

productivity of steelhead and spring and fall Chinook 

has decreased, although it is not yet clear why. It

appears possible that the amount of fine sediment has 

been decreased, perhaps by the 6 pulse flows that 

have occurred since the fire.

Fish and geomorphic monitoring results may 

improve future pulse flows. Results of pulse flows in 

FY 2010 suggested that higher flows would provide 

more favorable geomorphic outcomes. In addition,

it was determined that higher flows could have been 

provided without impacting the ability of the Clear 

Creek Community Services District to receive water. 

The 2010 results led to experimental flows in 2011, 

which were successful in achieving higher flows, and 

moving more sediment downstream. Therefore in 2012 

both higher and lower flows were provided. The Clear 

Creek Technical Team requested that NMFS modify 

the OCAP RPA I.1.1 to provide more flexibility and

aid in adaptive management. The proposal would 

allow the Clear Creek Technical Team to recommend 

to NMFS and Reclamation, changes in the timing, 

magnitude and duration of the spring attraction flows 

to better meet objectives of the Clear Creek RPA 

actions, additional ecosystem goals, operational 
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

constraints, and adaptive management. This proposal 

was prompted by the results from fish, geomorphic, 

avian and riparian monitoring. 

Fish Population Monitoring Suggests Program 

Success. Monitoring continues to document the overall 

success of the Clear Creek Restoration Program. 

No other Central Valley watershed has survived the 

Chinook fishery collapse nearly as well as Clear 

Creek. This may be due to increased resilience of the 

watershed due to CVPIA’s habitat restoration. In 2011

fall-run Chinook escapement was 4,841 compared to 

the average baseline escapement of 1,689 between 

1967 and 1991. Escapement appeared lower in 

2011 than in the previous 10-years (average of 

8,825), in part because the method for estimating 

escapement was changed. Using the old method the 

2011 escapement would be 6,332 (31% higher). In

addition, spawning populations of threatened spring 

Chinook and steelhead have been re-established in 

the watershed. 

The recent DFG Central Valley Steelhead Monitoring 

Plan and Central Valley Chinook Monitoring Plan 

recommended that a counting weir be used in Clear 

Creek to monitor adult populations of salmon and 

steelhead. In 2012 CVPIA partnered with DFG to buil

and install a fish counting weir in Clear Creek near the 

confluence with the Sacramento River. The weir will 

be operated year-round with DFG using it during fall 

Chinook passage and the FWS the rest of the year to 

monitor spring and late fall Chinook and steelhead. 

Downstream view of the Placer Bridge injection site, taken from the Vietnam Veterans Memorial ridge (aka Placer Bridge).
SPAWNING AND REARING HABITAT RESTORATION PROGRAM 3406 (b)(  

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 

potential to increase the quality and quantity of 

spawning and rearing habitat. Two criteria guide the 

identification of gravel placement sites: the need for 

spawning and rearing habitat; and accessibility to 

the river by heavy equipment, helicopter or sluice to 

deliver gravel or modify the channel.

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, topographic 

surveys, spawning surveys and rearing surveys. Once 

the gravel is placed, the SRHP monitors the spawning 

and rearing occurring at and near the restored sites 

and makes comparisons to pre-project conditions and 

control 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 (all Reclamation funded) 

conducted by the Department of Fish and Wildlife 

in the Sacramento, American and Stanislaus 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 but will occur in 2013. 

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 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 fish 

are successfully finding suitable sites to spawn and 

are spawning (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 2012 ACCOMPLISHMENTS 

In FY 2012, the SRHP obligated $758,228 from the

Restoration Fund.

Spawning and Rearing Habitat 

Restoration Program

 3406 (b)(13)
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Sacramento River – In 2012, the program placed

15,000 tons of gravel just below Keswick Dam, or 

150% of the annual target of 10,000 tons. This gravel 

is distributed downstream with high flows. Redd 

surveys funded separately by Reclamation showed 

that 66% of the winter-run Chinook salmon spawning 

occurred upstream of the Anderson Cottonwood 

Irrigation District diversion dam in 2012. This is the

reach affected by gravel injections at Keswick Dam 

and the section of river with the coolest water to 

support egg to fry survival.

Stanislaus River – In 2012, the program placed

3,000 tons of gravel at the Goodwin Canyon Float 

Tube Pool representing 100% of the annual target 

of 3,000 tons. Gravel was placed with the “Habitat 

Builder” just upstream of a riffle created in 2004 to 

increase the habitat available in this heavily utilized 

location. Habitat Builder is a gravel placement 

system where gravel is pumped through a pipe using 

water to tranport the gravel through to the desired 

location in the river. At the end of the pipe, people 

in the river guide the gravel slurry to the desired 

placement locations. This is the closest spawning riffle 

to Goodwin Dam (the top of anadromous habitat) and 

is in an area with a high density of rearing O. mykiss 

which are a threatened species in the Stanislaus. 

During redd surveys in fall of 2012, 139 Chinook 

salmon redds were mapped on the float tube pool 

riffles.

American River – In 2012, the SRHP placed

24,510 tons of gravel and created a 400-foot side 

channel at lower Sailor Bar. The gravel placement 

represented 350% of the annual target of 7,000 tons. 

This project was funded by SRHP, AFRP and the Corps 

of Engineers and included participation by multiple 

agencies including Reclamation, Fish and Wildlife 

Service, the Water Forum, City of Sacramento, CDFW, 

USACE, and Sacramento County Regional Parks. The 

project included a designed channel spanning gravel 

placement and a side channel incorporating woody 

material. A matrix of nine distinct gravel patches was 

included to test the performance of various gravel 

mixtures (i.e., sizes) between three different suitability 

ratings based on water velocity and depth. 

The program embarked on a Structured Decision 

Making process to help determine the most efficient 

use of management resources to maximize the 

number and condition of juvenile salmonids leaving 

the American River. We created a predictive model, 

parameterized primarily using expert opinion, 

representing the key variables that can be influenced 

by the gravel program. We are now quantifying the 

model functions using data and empirical models and 

will continue to update the model through focused 

project monitoring. The finished model is intended 

to be used as a decision support tool to assist in 

prioritization of sites for restoration (in-channel, side 

Crew placing gravel in the Stanislaus with the “Habitat Builder”.
SPAWNING AND REARING HABITAT RESTORATION PROGRAM 3406 (b)(  

FISHERIES

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

2012 15,000 150 3,000 100 24,510 350

TOTAL 203,961 127 29,100 61 84,880 76

Table 11: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2012

FWS crew laying out an experimental gravel patch as gravel 

placement proceeds at lower Sailor Bar.

Completed side channel at lower Sailor Bar.

channel, and floodplain) and the type of restoration 

action (gravel injection, gravel placement, in-channel 

or out-of-channel rearing habitat restoration) that will 

provide the greatest benefit to increase the number of 

juvenile outmigrants. 

Monitoring, using a before-after control-impact 

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.
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

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 2012 CAMP Annual Report provides data for 

22 Central Valley watersheds, and a broader area 

that includes San Pablo Bay, Suisun Bay, and the 

Sacramento-San Joaquin River Delta. The 2012 report 

is the tenth report prepared since 1992. 

The CAMP Implementation Plan identifies 82

monitoring elements that are required to assess 

progress toward the AFRP fish doubling goals. 

The plan describes these monitoring elements, 

and provides a framework to assess the biological 

response to, and effectiveness of, restoration actions 

(Objectives #1 and #2). The program goals have 

recently been expanded to consolidate, standardize, 

and enhance the collection of data related to the CVP 

ecosystems (Objective #3).

FY 2012 ACCOMPLISHMENTS 

In FY 2012, the CAMP received $3,621,718 from the

Restoration Fund.

Objectives #1

CAMP Annual Report: the development of the 2011 

version of the CAMP annual report was completed. 

The report is available at: http://www.fws.gov/

sacramento/Fisheries/CAMP-Program/DocumentsReports/Documents/2011_CAMP_annual_report.

pdf.

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. 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 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 was developed 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 

modifications, habitat restoration, and fish screens) 

toward meeting AFRP fish production targets.

Objective #3 – Establish a data management 

program to manage CVPIA data (a resource available

Comprehensive Assessment 

and Monitoring Program

 3406 (b)(16)
COMPREHENSIVE ASSESSMENT AND MONITORING PROGRAM 3406 (b)(1  

FISHERIES

Constant Fractional Marking Program: marking 

and tagging of juvenile fall-run Chinook salmon at the 

Nimbus Fish Hatchery and Coleman National Fish 

Hatchery was completed during the spring of 2012; a 

report documenting those operations is available at: 

http://www.fws.gov/sacramento/Fisheries/CAMPProgram/Documents-Reports/Documents/2012%20

Constant%20Fractional%20Marking%20Report.pdf.

Develop Report Documenting Adult Salmon 

Surveys On Cottonwood Creek: the development 

of a report documenting salmon video monitoring 

results from Cottonwood Creek between 2007 and 

2011 was completed. The report is posted on the 

CAMP’s website at http://www.fws.gov/sacramento/

Fisheries/CAMP-Program/Documents-Reports/

Documents/2007-2011%20Cottonwood%20

Creek%20video%20survey%20results.pdf.

Develop Report Documenting Adult Salmon 

Surveys On Cow Creek: the development of 

a report documenting salmon video monitoring 

results from Cow between 2006 and 2011 was 

completed. The report is posted on the CAMP’s 

website at http://www.fws.gov/sacramento/

Fisheries/CAMP-Program/Documents-Reports/

Documents/2006-2011%20Cow%20Creek%20

Video%20Survey%20Results.pdf.

Battle Creek Adult Chinook salmon escapement 

monitoring: surveys were conducted to quantify the 

abundance of adult Chinook salmon on Battle Creek. 

The surveys are conducted with a weir at the Coleman 

National Fish Hatchery. A report documenting the 

results from this activity will be completed in FY 2013.

Sacramento River Winter-run Chinook Salmon 

Escapement Surveys: a series of surveys were 

conducted to quantify the abundance of adult winterrun Chinook salmon in the Sacramento River mainstem. 

The surveys were conducted in partnership with the 

California Department of Fish and Wildlife. A report 

documenting the results from this activity will be 

completed in FY 2013.

Develop Analytical Framework And Tool To 

Develop Salmon Hatchery Proportions: a 

report providing an assessment of the feasibility of 

developing a spreadsheet/database quantifying the 

proportion of adult hatchery- vs. wild-origin Chinook 

salmon in watersheds and streams across the Central 

Valley was developed.

Finalize The Development Of The Chinookprod 

Database: supplemental funding was provided, 

and facilitated the conversion of the Chinookprod 

spreadsheet to a fully functional, fully documented 

database format.

Objective #2

CAMP Rotary Screw Trap Platform: work 

continued on the development of the CAMP Rotary 

Screw Trap Platform, and a final database structure 

for storing RST data has been created, a user interface 

with various forms for entering new RST data has been 

created, the migration of historical data from three 

watersheds to the CAMP database is nearly complete 

and the process of migrating historical data from 

two other watersheds is under way, and computer 

programming code is being developed that will 

produce juvenile salmon production estimates based 

on the raw data in the database.

Monitor Juvenile Chinook Salmon 

Production - Caswell State Park: rotary screw traps 

were operated at Caswell State Park on the Stanislaus 

River during all of the 2012 rotary screw trap field 

season; a report documenting those operations will 

be completed in late FY 2012. A report documenting 

the results from the 2010 and 2011 rotary screw 

trap field season was completed and is available 

on the CAMP’s website at: http://www.fws.gov/

sacramento/Fisheries/CAMP-Program/DocumentsReports/Documents/Stanislaus%20River%20

(Caswell)%20RST%20data%20(16)%202010%20

and%202011.pdf.

Monitor Juvenile Green Sturgeon And Chinook 

Salmon Abundance at the Red Bluff Diversion 

Dam: rotary screw traps were operated below the 

Red Bluff Diversion Dam on the Sacramento River 

mainstem on a nearly continuous basis. The trapping 

associated with that site is used to monitor the 

abundance of juvenile green sturgeon and four runs 

of Chinook salmon. A report documenting the results 

from this activity will be completed in FY 2013. 
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

Monitor Juvenile Chinook Salmon 

Production – Upper Battle Creek: rotary screw 

traps were operated on Battle Creek Dam during 

all of the 2012 rotary screw trap field season. The 

trapping associated with that site is used to monitor 

the abundance of three runs of Chinook salmon. A 

report documenting the results from this activity will be 

completed in FY 2013.

Objective #3 

Develop A Data Management Plan And 

Associated Data Documentation Forms: the 

program continued development of the CVPIA

data acquisition and management plan (DAMP). In

addition to a plan describing laws, requirements, 

and associated protocols, the program has designed 

and created a DAMP Excel workbook as an aid in 

documenting CVPIA data sets. Meetings were held

presenting the workbook to program managers to 

obtain feedback and guidance. Program managers’ 

recommendations are currently being reviewed for 

implementation.

GIS Network Access Tool (GNAT): a tool to access 

the CVPIA document data base is under development

by the BOR. This tool will allow users to access CVPIA

documents according to location, topic, and program 

activity via an interactive, web-accessible graphical 

user interface (GUI). The tool will have the look and

feel of a GIS tool. Deployment of this tool is scheduled

for FY 2013.

Other Data Management: an Excel workbook was 

designed and created that allows entry of program 

activities and associated information (funding levels 

and source, responsible agencies, etc). Pre-formatted 

tables are easily created for input into the annual work 

plans. 

Performance Goals And Accomplishments: the 

various program goals and annual accomplishments 

were compiled and included in a central Excel 

workbook. The information was reviewed by program 

managers.
ANADROMOUS FISH SCREEN PROGRAM 3406 (b)(21) 4

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 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 many diversions and fish screens to determine the 

critical factors related to fish losses, and to assure 

the effectiveness of constructed fish screens. Fish 

screen projects are typically complex, and are often 

constructed in phases over several years. The three 

key project phases include feasibility, 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 conducting fish entrainment monitoring 

at representative unscreened diversions on the 

Sacramento River to evaluate potential fish screening 

benefits and to help determine the highest priority 

diversions for screening.

FY 2012 ACCOMPLISHMENTS 

The AFSP obligated funding from the Restoration Fund 

in the amount of $6,014,000, $4,300,000 from the 

Water and Related Resources Fund, $1,500,000 from 

Bay-Delta funds, and $1,914,000 from State matching 

cost-share funds. 

Screening Diversions – Construction was initiated 

on the Yuba City Fish Screen consisting of a 74 cfs 

diversion on the Feather River. This project will be 

completed in FY 2014. 

Construction continued on the Natomas Mutual 

Sankey Fish Screen project for a 389 cfs screened 

diversion 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. Also, environmental 

compliance and design work continued on the Phase 

2A project to screen a Natomas Mutual 150 cfs 

diversion at Pritchard Lake on the Sacramento River. 

The AFSP continued to support design, environmental 

compliance, and permitting activities for the RD 2035/

Woodland Davis Clean Water Agency Joint Intake

and Fish Screen project on the Sacramento River. This 

fish screen project is targeted to begin construction in 

FY 2014.

Anadromous Fish Screen 

Program

 3406 (b)(21)
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

fish screens: Feather Water District North (78 cfs) and 

South(40 cfs) on the Feather River, South Sutter #1 (80 

cfs) on Auburn Ravine, and Colusa Indian Community

Council Compton (22 cfs) on the Sacramento River. 

(see Table 12 for projects by watershed).

AFSP Technical Assistance – The AFSP continued a 

three-year (2010-2012) 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 is also evaluating 

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.

The AFSP continued to support design, environmental 

compliance, and permitting activities for the West 

Stanislaus Irrigation District Fish Screen Project off the

lower San Joaquin River. This fish screen project is 

targeted to begin construction in FY 2015 or 2016.

The AFSP completed construction of the Bella Vista 

Fish Screen, involving installation of state-of-the-art 

retractable cylindrical fish screens at the existing 85 cfs 

pumping plant on the Sacramento River near Redding. 

In addition, an existing RD 108 South Steiner 30 cfs

diversion on the Sacramento River was permanently 

removed, and pipeline facilities were constructed to 

allow the area previously served by the South Steiner 

diversion to use irrigation water pumped from the 

existing RD 108 Wilkins Slough Pumping Plant and 

Fish Screen.

Project implementation continued on five fish screens: 

River Garden Farms #3 at Townsite (62 cfs), Cranmore 

Farms #2 (36 cfs), Tisdale #2 (44 cfs) and Alamo 

Farms #1 (36 cfs) on the Sacramento River, and Joe 

Sanchez Farms (24 cfs) on Steamboat Slough in the 

Sacramento-San Joaquin Delta. Fish entrainment 

monitoring was also conducted in 2012 at these 

five diversion locations prior to installation of the fish 

screens. This effort is part of a program to collect 

data to assess the biological benefits of fish screening 

and to help prioritize future fish screening efforts. In

addition, project implementation continued on four 

Table 12: AFSP Projects by Watershed 

and Cubic Feet per Second (cfs) 

Screened, 1994-2012

Watershed

Number of

 Fish Screens

Flow

(cfs)

Sacramento 21 4,212

American 1 310

Yuba 1 65

Butte 4 257

Delta 6 113

San Joaquin 2 455

TOTAL 35 5,412
SAN JOAQUIN RIVER RESTORATION PROGRAM PUBLIC LAW 111  

FISHERIES

funds from the State of California, and funds from 

the CVP Restoration Fund. Actions to implement the 

Settlement will also be accomplished with in-kind 

services conducted by the State of California through 

the Department of Water Resources and Department 

of Fish and Wildlife. This description of program 

goals and objectives is intended to focus on those 

activities that are anticipated to be implemented using 

funds from the CVP Restoration Fund. See the Annual 

Report published by the San Joaquin River Restoration 

Program for a description of all of the Program’s 

activities (annual reports are available at www.

restoresjr.net). 

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 2012 ACCOMPLISHMENTS 

The Program obligated $2,599,325 from the CVP 

Restoration Fund to achieve the following:

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 Wildlife (CDFW). 

Actions to implement the Settlement are anticipated 

to be funded using four different funding sources in 

FY 2014. These include mandatory and appropriated 

funds in the San Joaquin River Restoration Fund, 

San Joaquin River Restoration 

Program

 Public Law 111-11
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

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 2012 

Interim Flows, and specifically, as part of Reclamation’s

Water Year 2012 Interim Flows Environmental

Assessment (EA). In FY 2012, the SJRRP awarded

a grant to the San Joaquin River Parkway and 

Conservation Trust, Inc. to help fulfill these invasive

vegetation monitoring and management commitments. 

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. 

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 process 

to identify study needs and monitoring activities and 

providing timely release of all quality controlled 

monitoring data. In FY 2012, Reclamation funded

the Annual Technical Report (ATR) and Monitoring 

and Analysis Plan (MAP) efforts. These efforts include 

coordinating the SJRRP’s Restoration Goal Technical 

Feedback Group meetings that facilitate the timely 

public release and discussion of monitoring data, 

upcoming monitoring efforts, and provide for early 

input to the Program’s high priority construction 

projects. The outputs from these efforts were the 

2011 ATR in March 2012 and the Final 2012 MAP in 

November 2011.

Fish Population Modeling – In FY 2012 and in

support of the Restoration Goal, Reclamation issued 

a contract to develop a fisheries population model 

to support the continued development of the SJRRP 

Fisheries Management Plan and to inform the selection 

of alternative actions, which include the release 

and routing of flows, salmon reintroduction, and 

construction of site-specific projects. The modeling 

effort will utilize the Ecosystems Diagnosis and 

Treatment (EDT) modeling platform and “proof of 

concept” model previously prepared for the San 

Joaquin River. The effort will apply the EDT model 

to addressing fish management questions and sitespecific planning and evaluation needs as well as 

improve the model.

The above accomplishments were achieved with 

CVPIA funding. To see all SJRRP accomplishments, visit

www.restoresjr.net. 

In this photo, a fisheries biologist from Reclamation’s Technical Service Center in Denver makes a small incision in a juvenile fallrun Chinook salmon and, at bottom right, inserts a small tag as part of a study supporting reintroduction of Chinook salmon into 

the San Joaquin River. 
ECOSYSTEM AND WATER SYSTEMS OPERATIONS MODELS 3406 (g) 4

FISHERIES

(3) completed modeling for the Interim SWRCB San

Joaquin Flow Standards EA; (4) made various CalSim 

II modification  to rectify logic that was found to caus

unintended effects, to adapt existing logic to changed 

assumptions that governs the model inputs and to 

expand the model’s logic to reflect new physical and/

or regulatory conditions; (5) developed the model 

and investigated the effects on Central Valley from 

BDCP Alternate 8 (aka SWRCB Alternative), Sisk Dam 

Corrective Action Studies, and North Bay Aqueduct 

Alternate Intake projects. These modifications

facilitate the use of the model for numerous studies 

by Reclamation and others which ultimately lead to 

increased understanding referenced in §3406(g).

CalLite accomplishments for FY12 included (1) 

finalized development of CalLite 2.0 and made it 

publicly available from California Department of 

Water Resources (DWR) website. In doing so, licenses

to use the associated numerical solver were integrated 

into the model, thereby making CalLite 2.0 free to the 

user community; (2) conducted two training sessions, 

one for Reclamation and DWR and one for state and 

Federal fish agencies. Besides keeping the model 

relatively simple, this training helped make CalLite 

readily usable; (3) made various CalLite modifications 

to rectify logic that was found to cause unintended 

effects, to adapt existing logic to changed input 

assumptions and to expand the model’s logic to 

reflect new physical and/or regulatory conditions. 

These modifications facilitate the use of the model for 

numerous studies by Reclamation and others which 

ultimately lead to increased understanding referenced 

in §3406(g); (4) implemented D1485 regulations and 

made the model able to evaluate their impacts on 

water supply and Delta exports; (5) added Dynamic 

Allocation Procedure (DAP) in CalLite model.

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 Interior will develop data and/or models to

improved scientific understanding in nine integral 

areas. 

FY 2012 ACCOMPLISHMENTS 

The Modeling Program obligated $554,129 from the 

Restoration Fund in FY12. 

CalSim I accomplishments for FY12 included (1

developed a new and improved CalSim Benchmark 

Study to establish a CalSim baseline that can be used 

for planning and other studies; (2) updated CalSim 

II models for the Shasta Enlargement Project E

alternatives to match the current CalSim baseline and 

improve operations of the enlarged Shasta Reservoir; 

Ecosystem and Water Systems 

Operations Models

 3406 (g)
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

FISHERIES

CalSim 3.0 accomplishment for FY12 included (1) 

continued to refine/calibrate/validate hydrology 

and stabilized the model for Sacramento Valley for 

the beta release; (2) refined ground water Dynamic 

Link Library (DLL) implementation in CalSim 3.0; 

(3) continued to refine the CalSim 3.0 schematic/

presentation tool; (4) developed model diagnostic/

presentation toolbox; (5) started merging with SJR 

module; (6) expanded model domain; (7) developed 

2030 hydrology; (8) updated Delta land uses, etc.

HEC-5Q temperature model accomplishment for 

FY12 included (1) extended the model to include 

the Sacramento River to above Ord Ferry; four 

weirs (Moulton, Colusa, Tisdale, and Fremont); and 

the Sutter Bypass that will allow to complete the 

Sacramento River flow accounting and to provide 

computed temperature at the Feather–Sutter Bypass 

confluence; (2) implemented the HEC-RAS model for 

the Bypass–Feather–Sacramento–American system 

and prepared HEC-5Q-compatible cross-section 

inputs; (3) developed 1920-2012 meteorological 

inputs from CIMIS data at the Nicolas, Colusa, an

Fair Oaks stations; (4) processed flow and operation 

data for the Folsom–Natoma– American River system; 

(5) converted the Folsom Lake temperature profile 

spreadsheet data to model-compatible DSS data; (6) 

developed Folsom Lake and Lake Natoma model 

data, including representation of the Folsom Dam 

temperature control device (TCD); (7) performed 

initial calibration of Folsom Lake using monthly 

profile and release temperature data; (8) refined 

representation of the Oroville–Thermolito facilities; 

(8) developed stage-flow (H-Q) relationships for 

defining downstream-reach control elevation for the 

HEC-RAS model; (9) simulated a series of flows with 

the HEC-RAS model for defining the depth-area-widthflow tables required by SRWQM; (10) generalized 

the utility program that converts American River 

HEC-RAS output to SRWQM inputs; (11) refined 

initial calibration of the American River using the 

HEC-RAS based geometry data; (12) Modified the 

HEC5Q source code to provide summary output for 

analyzing Folsom Dam temperature control device 

(TCD) structure operation, (13) processed additional 

inflow temperature data for model calibration; and 

(14) revised reservoir release algorithm for revised 

temperature objectives for Folsom Dam outflow.

C2VSIM (California Central Valley GroundwaterSurface Water Simulation Model) accomplishment

for FY12 included (1) released IDC (IWFM Deman

Calculator) version 4.0.226 to the public in May 

2012; (2) released generic surface water-groundwater 

model engine Integrated Water flow Model (IWFM

version 4.0 to the public in July 2012; (3) completed 

C2VSIM draft report for the historical simulation

1922-2009 and associated appendixes; (4) 

developed a fine grid version of the C2VSIM model

for the historical simulation 1922-2009 (resolution 

averages less than a square mile per element). It is

expected to be released early 2013; (5) participated 

in the on-going CWEMF-sponsored peer review of 

the IWFM, HydroGeoSphere, and MODFLOWFMP integrated hydrologic models; (6) assisted UC

Davis in implementing IDC v 4.0 to Fabian Tract in

the Delta and in organizing a CWEMF sponsored 

public workshop at UC Davis in August 2012 (7) 

implemented the San Joaquin portion of C2VSIM into

CalSim 3.

ANN Model accomplishment for FY12 was that the 

robustness of the trained ANN for CalSim 3 base 

case was tested and training data requirements were 

identified.

DSM2 model accomplishment for FY12 included 

(1) improved channel geometry in the model and 

recalibrated DSM2 version 8.1 by adjusting Manning’s 

coefficient values, (2) studied the South Delta null 

zones to analyze whether and to what extent CVP and 

SWP exports and the agricultural temporary barrier 

influence the stage and circulation; and (3) Improved

DSM2 particle tracking modules.

inSALMO accomplishment for FY12 included (1) 

investigated how spatial resolution of the input data 

affects model results by procuring depth, velocity, and 

habitat data and extending the model to new river 

reaches; (2) continued to develop model parameters 

to enable inSALMO to simulate steelhead spawning, 

egg incubation, emergence and rearing; (3) further 

calibrated and validated the model with aforesaid 

data; and (4) submitted a manuscript entitled 

“Railsback, S. F., M. Gard, B. C. Harvey, J. L. White, 

and J. K. H. Zimmerman, Evaluation of a salmon 

habitat restoration project using an individual-based 

model” on June 23, 2012, to North American Journal 

of Fisheries Management. 
ECOSYSTEM AND WATER SYSTEMS OPERATIONS MODELS 3406 (g) 5

FISHERIES

Table 13: Ecosystem and Water System Operations Models Developed To Date

Model Type Models Developed To Date

Comprehensive water budget of surface and groundwater 

supplies 

CalSim II, CalSim 3.0 CalLite, HGS, ANN, ECOSIM-W, 

C2VSIM and DSM2

Related water quality conditions, including temperature 

dynamics related to storage

Upper Sacramento River Water Quality Model (SRWQM). San 

Joaquin Basin Temperature Model HEC-5Q

Surface-ground and stream-wetland interactions HydroGeoSphere, CVHGSM (Central Valley HydroGeoSphere 

Model), C2VSIM

Ecosystem modeling - flow needs to meet restored carrying 

capacity of streams

inSALMO

Ecosystem modeling - flow to store and maintain natural 

channel and riparian habitat values

RHEM

Water operations models - CVP and SWP operations CalSim II, CalSim 3.0 CalLite and ECOSIM-W

Ecosystem modeling in support of sustainable fish harvest 

levels, including tradable harvest rights 

None

Ecosystem modeling to identify opportunities to protect and 

restore wetland and upland habitat

inSALMO

Water management modeling to include firm CVP yield CalSim II, CalSim 3.0, CalLite and ECOSIM-W

HydroGeoSphere (HGS) accomplishment for FY12 

included (1) developed a groundwater (subsurface 

flow only or variably-saturated flow) model capable 

of evaluating the impact of groundwater withdrawal 

on land subsidence in the San Joaquin River basin; 

(2) extended the groundwater model to surface/

subsurface flow model by including application of 

surface-flow and parallelization capabilities. 

The 3406 (g) program also prepared publications 

and provided support to model applications for 

stakeholders. Table 13 presents the nine model types 

and FY12 accomplishments.

All of the projects that were undertaken in FY2012 met 

or exceeded the performance targets.

Chapter 3

CVP WATER 

OPERATIONS

RESOURCE 

AREA

Central Valley Project Improvemen
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

WATER OPS

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.

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. 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 Incrementa

Methodology (IFIM) studies, undertaken as par

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-controlle

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 Reservoi

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/o

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 is reduced by up

to 100,000 AF. In critically dry years, the target is

reduced by up to 200,000 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 2012 ACCOMPLISHMENTS 

The program obligated $776,136 from the Restoration 

Fund in FY 2012. 

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 2012 was the driest since the 2007-

2009 drought. Near record dry conditions during 

Dedicated 800,000 acre-feet 

Project Yield

 3406 (b)(2)
DEDICATED 800,000 ACRE-FEET PROJECT YIELD 3406 (b)(2  

WATER OPS

the winter precipitation months were followed by 

an unseasonably wet late spring. The final Water 

Year 2012 classification was below-normal for the 

Sacramento Valley and dry for the San Joaquin Valley. 

Impacts of the dry year were somewhat minimized due

to the good carry-over storage from WY 2011.

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

fish actions in water year 2012. Table 14 presents the 

historic allocation and use of (b)(2) water. Table 15 

summarizes how (b)(2) water was used in 2012 for fish 

and wildlife 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 

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 14: Allocation Target and Use of (b)(2) Water, 2001-2012

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

2012 Below Normal 800,000 800,000

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

** 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.
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

WATER OPS

River Action Timeframe Results

American (b)(2) water used to augment 

would-be base flows to maintain 

1100 - 2500 cfs

November 2011 - 

March 2012

Contributed toward AFRP Final Restoration Plan flow 

objectives and improved instream conditions for fallrun Chinook and steelhead spawning, rearing, and 

outmigration.

Clear Creek AFRP under (b)(1) authority and 

(b)(2) water used to augment 

would-be base flows throughout 

water year 2012

October 1, 

2011 – September 

30, 2012

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 2012 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 

3300 - 5800 cfs

December 2011 - 

February 2012

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 provide 

outmigration pulse flow

April 2012 - June 

2012

Contributed toward AFRP Final Restoration 

Plan flow objectives and provided pulse flow for 

juvenile steelhead and fall-run Chinook rearing and 

outmigration. 

CVP Jones 

Pumping 

Plant

CVP exports were reduced 

pursuant to the NMFS BO.

February 2012 – 

June 2012

Benefitted outmigrating salmon and steelhead 

smolts. Concurrent benefits to delta smelt.

Table 15: FY 2012 Use of (b)(2) Water by Location
WATER ACQUISITION PROGRAM - INSTREAM WATER 3406 (b)  

WATER OPS

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 2012 ACCOMPLISHMENTS 

The Instream WAP obligated $1,983,287 from the

Restoration Fund and $175,000 from the Water and 

Related Fund. The Instream WAP used this funding to

acquire a total of approximately 25,714 AF.

Table 16 shows the instream water acquisitions from 

1994-2012.

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 manages a two year agreement

(2012-2013) with the Merced Irrigation District to

provide additional spring fishery flows on the Merced, 

and lower San Joaquin rivers. The flows are used in 

support of out migrating juvenile salmonoid in the 

spring. 

Water acquisition for CVPIA-designated refuges and

wildlife management areas is discussed in Section 

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

(Refuge WAP).

Water Acquisition Program – 

Instream Water

 3406 (b)(3)
58 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

WATER OPS

Table 16: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 

 1994-2012

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

2012 25,714 13

Average 78,576 39
FLOW FLUCTUATIONS AND RESERVOIR STORAGE 3406 (b)(9) & (19  

WATER OPS

FY 2012 ACCOMPLISHMENTS 

The FFP obligated $14,779 from the Restoration Fund 

in FY 2012. 

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 2011-2012 on Clear Creek, the American 

River, and the Sacramento River. Surveys began in 

mid-December and continued through the end of the 

spawning season (mid-April). Insights gained will help

make informed decisions pertaining to flow fluctuations 

as well as the potential use of (b)(2) dedicated yield.

American River – Two salmonid isolation pool 

surveys were conducted in May 2012 and multiple 

steelhead redd surveys took place December 2011 

through April 2012. In the isolation pool surveys, a

small number of steelhead and Chinook salmon were 

observed. No rescue measures were implemented 

because the pools reconnected shortly after the 

surveys were conducted. 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 CDFW. The group also 

helped coordinate fish monitoring studies and habitat 

mapping. 

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, the 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, CDFW 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. 

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

(AF) of carryover storage levels at Shasta Reservoir 

and 600,000 AF at Trinity River Reservoir. 

Flow Fluctuations and Reservoir 

Storage

 3406 (b)(9) & (b)(19)
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

WATER OPS

Table 17: Carryover Storage at Shasta and Trinity Reservoirs, 1998-2012

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

2012 Below Normal 2.6 MAF 1,800 TAF

* million acre-feet

** thousand acre-feet

Carryover Storage

The RSP met the carryover targets for Shasta and 

Trinity reservoirs in FY 2012 with 2.592 MAF and 

1.800 MAF, respectively (see Table 17 ). 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.
CONTRACT RENEWALS AND WATER TRANSFERS 3404 (c) and 3405 61

WATER OPS

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 28 

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. 

Execution of the remaining contract renewals is 

pending completion of the court-directed BO. 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 and industrial 

demands, as well as provide environmental and 

recreational benefits. 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 2012: 

•	271,632 AF of CVP agricultural water was 

approved for agricultural purposes

•	92,916 AF of CVP agricultural water was 

approved for agricultural purposes (Recaptured 

Water Account (RWA))

•	10,000 AF of CVP municipal and industrial 

water was approved for agricultural purposes 

(Recaptured Water Account (RWA))

•	650 AF of CVP municipal and industrial water 

was approved for municipal and industrial 

purposes (Recaptured Water Account (RWA))

•	100,000 AF of CVP agricultural water was 

approved for municipal and industrial purposes 

(Metropolitan Water District)

•	1,300 AF of CVP agricultural water was 

approved for municipal and industrial purposes

Contract Renewals and Water 

Transfers

 3404 (c) & 3405
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

WATER OPS

•	13,100 AF of CVP municipal and industrial 

water was approved for agricultural purposes

•	34,438 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.
Central Valley Project Improvemen

Chapter 4

REFUGES

RESOURCE 

AREA
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

REFUGES

The Refuge Water Supply Program (RWSP) is 

comprised of three components: 

3406 (d)(2) 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.

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 7). 

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 differenc

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 

Refuge Water Supply Program

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

REFUGES

Department of Fish and Wildlife (CDFW), the Service, 

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 IRWMT is comprise

of representatives from Reclamation, the Service, 

CDFW, 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 

2012, 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 2012, 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 (GRCD). 

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 2012 ANNUAL REPO

REFUGES

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

Mendota Wildlife Area

Gray Lodge

Wildlife Area

Sutter National

Wildlife Refuge

Pixley National Wildlife Refuge

Kern National Wildlife Refuge

Sacramento National

Wildlife Refuge

CVPIA 

REFUGES

Sacramento

San Francisco

Los Angeles

Volta Wildlife Area

Delevan National 

Wildlife Refuge

Colusa National

Wildlife Refuge
WATER ACQUISITION PROGRAM - REFUGE WATER 3406 (d)(  

REFUGES

The Refuge Water Acquisition Program (RWAP) is 

responsible for the acquisition of133,264 acre-feet 

(AF) of Incremental Level 4 (Inc L4) Water (als

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, Inc L4 water consists of 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 other groundwater wells 

including two new groundwater wells constructed at 

the Volta Wildlife Area under the American Recovery 

and Reinvestment Act. The groundwater wells will 

increase water supply reliability and help to diversify 

Level 2 Water. It is anticipated that together these wells

will produce up to 10,000 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 2012 ACCOMPLISHMENTS 

The RWAP obligated $6,662,257 from the Restoration 

Fund. Funds were used to support Real-time Water 

Quality Monitoring project, South-of-Delta (SOD) 

coordinator, groundwater assessment, and program 

administration.

The RWAP purchased 47,263 AF of water for Water 

Year 2012. This water was acquired for delivery in the 

2012 water year which covers a portion of calendar 

year 2012 and a portion of calendar year 2013 

(March 1 – February 28).

Refuge Water Acquisition

 3406 (d)(2)

Snow Geese, Sacramento NWR
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

REFUGES

Table 18: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2012

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

2012 54,013 41

Average 63,782 48

* 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 47,263 AF of purchased water was acquired 

from a variety of surface and ground water sources. 

An additional 6,750 AF of water was acquired 

without cost to Reclamation. Both purchased and 

no-cost supplies brought the Inc L4 water to 54,013

AF which includes water to account for conveyance 

losses such as seepage and evaporation. Of the 

54,013 AF, approximately 42,494 AF of Inc L4 water

was actually delivered to the nine SOD refuges and 

1,450 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.
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 69

REFUGES

The Refuge Water Conveyance (Wheeling) 

Component (RWCC) 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 RWCC has two 

primary performance goals, specifically, starting with 

Water Year 2002 forward: 

•	Annually provide/deliver Level 2 (L2) water 

supplies by specified amounts to the refuges 

totaling 422,251 acre-feet; and

•	Annually deliver Inc L4 acquired water supplies

by specified amounts to the refuges totaling 

133,264 acre-feet.

The RWCC delivers L2 and Inc L4 water supplies to

the refuges through agreements with water conveying 

entities. Established refuge allocations for L2 and Inc

L4 water supplies serve as the Program’s goals for 

water conveyance quantities. 

Reclamation entered into five long-term water supply 

contracts -- one with GWD, two with the Service, and 

two with CDFW -- which established Reclamation’s 

commitment to the CVPIA delivery mandates.

Reclamation currently has eight long-term (15-50 

years) conveyance agreements that are administered 

by the RWCC, along with one FWS 40-year 

conveyance agreement, also administered under the 

RWCC. The RWCC utilizes cooperative agreements to 

reimburse delivering entities for costs of conveying L2 

and Inc L4 water supplies through federal, state, and

private water distribution systems to the refuges. 

PERFORMANCE MEASURES 

Delivery – The RWCC goal is to deliver L2 water 

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

26,007 AF of replacement water); and Inc L4 water of

133,264 AF per year.

A portion of L2 water supplies is provided from 

non-CVP diverse sources which assists in minimizing 

possible adverse effects on other CVP contractors.

FY 2012 ACCOMPLISHMENTS 

The program obligated $11,360,280 from the 

Restoration Fund.

Delivery – In 2012, an estimated 402,454 AF of L2

water was delivered to the refuges, representing 95% 

of the target (Table 19).

An estimated total of 55,515 AF of Inc L4 water was

delivered, representing 42% of the target. Table 20 

shows the targets and deliveries for each refuge for the 

2012 Fiscal Year.

Diversification – Of the total of 402,454 AF of L2 

water delivered in 2012, a total of 39,064 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.

Refuge Water Conveyance

 3406 (d)(1), (2) & (5)
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

REFUGES

Fiscal 

Year* L2 Delivered

% 422,251 AF 

L2 Goal** Inc L4 Delivered

% 133,264 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

2012 402,454 95 55,515 42 457,969 82

Average 

Deliveries

383,081 91 68,269 51 451,350 81

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

 [Section 3046 (d)(2)]. 

** L2 goal includes approximately 26,000 AF of replacement water.

*** Inc L4 goal does not include replacement water.

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

2002-2012
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 71

REFUGES

Table 20: Water Targets and Deliveries for Each Refuge (FY 2012)

WATER ALLOCATION TARGETS 2012 DELIVERIES % TARGET ACHIEVED***

Refuge Name - 

Region

Level 2 

Water (AF)*

Inc L4 

Water 

(AF)**

Full level 4 

Water (AF) 

(= L2+Inc 

L4)

Level 2 

Water 

(AF)

Inc L4 

Water 

(AF)

Total 

Delivered 

(AF) 

(= L2+Inc L4)

Level 2 

Water (%)

Inc Level 4 

Water (%)

Full 

level 4 

Water (AF) 

(= L2+Inc 

L4)

Grassland Water District (private) — San Joaquin Valley

Grassland RCD 125,000 55,000 180,000 136,529 28,146 164,675 109 51 91

CA Department of Fish and Wildlife — Sacramento Valley

Gray Lodge WA 35,400 8,600 44,000 31,612 0 31,612 89 0 72

CA Department of Fish and Wildlife — San Joaquin Valley

Volta WA 13,000 3,000 16,000 10,324 2,489 12,813 79 83 80

Los Banos WA 16,670 8,330 25,000 16,465 4,221 20,686 99 51 83

Salt Slough Unit 6,680 3,340 10,020 8,045 1,179 9,224 120 35 92

China Island Unit 6,967 3,483 10,450 7,948 920 8,868 114 26 85

Mendota WA 27,594 2,056 29,650 29,646 1,614 31,260 107 79 105

U.S. Fish and Wildlife Service — Sacramento Valley

Sacramento 

NWR 46,400 3,600 50,000 41,077 0 41,077 89 0 82

Delevan NWR 20,950 9,050 30,000 20,443 3,250 23,693 98 36 79

Colusa NWR 25,000 0 25,000 20,019 0 20,019 80 N/A 80

Sutter NWR 23,500 6,500 30,000 11,553 0 11,553 49 0 39

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

San Luis Unit 19,000 0 19,000 22,769 0 22,769 120 N/A 120

Kesterson Unit 10,000 0 10,000 10,907 0 10,907 110 N/A 110

West Bear Creek 

Unit 7,207 3,603 10,810 6,975 0 6,975 97 0 97

Freitas Unit 5,290 0 5,290 5,969 0 5,969 113 N/A 113

Merced NWR 13,500 2,500 16,000 16,126 2,500 16,126 119 100 101

East Bear Creek 

Unit 8,863 4,432 13,295 3,719 0 3,719 42 0 28

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

Kern NWR 9,950 15,050 25,000 4,147 11,196 15,343 42 74 61

Pixley NWR 1,280 4,720 6,000 681 0 681 53 0 11

TOTAL 422,251 133,264 555,515 402,454 55,515 457,969 95 42 82

* 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 2012 ANNUAL REPO

REFUGES

The Refuges Facilities Construction Component (RFCC) 

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 RFC

is responsible for the delivery of water to those lands 

identified in the Report on Refuge Water Supply 

Investigations (March 1989)(Report) and the San

Joaquin Basin Action Plan/Kesterson Mitigation Action 

Plan (December 1989)(Plan). 

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 RFCC is 

to have the necessary facilities in place for delivery of 

Full Level 4 (FL4) water supplies to the CVPIA refuges,

meeting their timing and scheduling requirements. A 

FL4 water supply will support optimum wildlife habitat 

over a broad range of species including targeted 

Threatened and Endangered species. 

The RFCC identified a total of 46 major structures and/

or actions (Projects) necessary to provide needed 

capacity for the delivery of FL4 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 refuge lands 

indentified in the Plan and 26 Projects are associated 

with refuges identified in the Report. Those refuges 

still requiring conveyance facility improvements are: 

Gray Lodge and Mendota WAs, and Sutter and Pixley 

NWRs. 

An Implementation Plan for refuges identified in the

Plan was completed in April 1998, and cooperative 

agreements with the San Luis Canal Company, GWD, 

and Central California Irrigation District to convey

water to these refuges were completed in summer 

1998. Reclamation is currently administering the 

cooperative agreements, which include construction 

and rehabilitation of facilities to accommodate the 

needs of these refuges. 

RFCC activities include project integration and 

coordination with the associated Refuge Water 

Conveyance Component (RWCC) and Refuge 

Water Acquisition Component (RWAC) to ensure 

continuity of methodologies and approaches 

towards executing and achieving RFCC objectives. 

Interagency coordination activities are included in

this element as well as budget formulation, tracking, 

and management activities. Additional activities are 

coordinating planning, design, and construction 

efforts between agencies and water purveyors (water 

districts). Reclamation’s Mid-Pacific Construction 

Office (MPCO) provides assistance to the RFCC by 

administering 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.

PERFORMANCE MEASURES 

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

refuges have the external conveyance capacity to 

Refuge Facilities Construction 

Component

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

REFUGES

receive FL4 Water, totaling 555,515 acre-feet (AF), on 

an annual basis.

FY 2012 ACCOMPLISHMENTS 

In FY 2012, the RFCC obligated $138,073 from the

Restoration Fund and $130,323 from the Water and 

Related Resources in support of refuges identified in 

the Plan. In addition, the RFCC obligated $493,849

from the Restoration Fund and $89,746 from ARRA in 

support of refuges identified in the Report. Total funds 

available for the construction of refuge conveyance 

facility projects in FY 2012 were $852,068.

In FY 2012, the RFCC contracted for services to

provide ongoing repairs to the East Bear Creek Unit of 

the San Luis National Wildlife Refuge Complex (East 

Bear Creek) Pumping Plant. Repair work performed 

kept the pumping plant operational during FY2012. 

Other modifications at this pumping plant to improve 

its reliability are expected to be completed in FY 2013. 

In FY 2012, the RFCC, in conjunction with the RWCC,

completed construction of the Gray Lodge and Pixley 

Groundwater Well Projects, which were funded under 

the American Recovery and Reinvestment Act (2009) 

(ARRA). Two wells were installed at Pixley NWR, and 

will provide for full L2 water supplies. Three wells were 

installed at Gray Lodge WA and will provide a portion 

of this refuge’s L2 supplies. Modifications to these wells 

are expected to be completed in FY 2013 to ensure 

their full functionality. 

Also under ARRA, Reclamation completed the 

construction of four new groundwater production 

wells at the GRCD. One half of the water from these 

groundwater production wells will provide IL4 water

supplies to GRCD, state, and federal CVPIA refuges

on the west side of the San Joaquin Valley. The 

remaining half of the water will help diversify refuge L2 

water supplies in accordance with CVPIA.

In addition, for the Gray Lodge WA, the final design

of the Biggs-West Gridley Water District (BWGWD) 

Facilities Improvement Project was completed in FY

2012. Construction of this project is expected to 

commence in FY 2013. When completed, which is 

anticipated in FY 2015, BWGWD will have sufficient 

conveyance capacity for FL4 water deliveries to the 

Gray Lodge WA. 

For each of the 19 CVPIA refuges, the conveyance

target and actual conveyance capacity are shown in 

Table 21.
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

REFUGES

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

Refuge Name - Region

Target FL4 

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 Wildlife – Sacramento Valley

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

CA Department of Fish and Wildlife – 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 2012 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 a 

large part of the Central Valley as a result of CVP 

construction and operation, 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 to 

listed species are significant. The program also focuses 

on restoration of CVP-affected habitats, and research 

to facilitate species recovery. In addition, the HRP

supports captive propagation and reintroduction of 

federally listed species affected by the CVP. 

PERFORMANCE MEASURES

Protection and Restoration – The program 

contributes to the protection and restoration of 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 

Habitat Restoration Program

 3406 (b)(1) “Other”

Endangered Metcalf Canyon jewelflower. Project entails introduction of the jewelflower to County lands at Tulare Hill, and 

supplementation of existing populations at Motorcycle County Park, in Santa Clara County. 
HABITAT RESTORATION PROGRAM 3406 (b)(1) “Other  

HABITAT

Place of Use, Habitat Mitigation Plan and Monitoring 

and Reporting Program (HMP) as a report/strategy 

of how the mitigation requirements will be addressed. 

The HMP identifies acquisition, maintenance, and 

restoration of 45,391 acres needing to occur as 

mitigation as part of the 2.7 million acres affected 

by the CVP. See Table 22 for acres protected and 

restored from 1996 through 2012.

Other Activities – The program also provides funding 

to support the recovery of threatened and endangered 

species through activities such as research and captive 

propagation and reintroduction. In part, research

proposals must describe how project deliverables 

would increase current and future protection and/

or restoration of species or habitats impacted by the 

CVP. For captive propagation and reintroduction 

projects, reintroductions on lands that are protected in 

perpetuity, and specifically managed for the benefit of 

the species, receive priority consideration of funding 

within that category of activities.

FY 2012 ACCOMPLISHMENTS 

The program obligated $1,485,765 from the 

Restoration Fund to achieve the following: 

Protection and/or Restoration – The HRP funding 

helped protect 2,333 acres of land through fee title 

acquisitions of 520 acres of alkali scrub, grassland, 

and riparian woodland habitats in Fresno County; 

1,615 acres of alkali scrub and grassland habitats in 

Kern and San Luis Obispo counties; and 198 acres 

of grassland habitat in Tulare County. Nine hundred 

and thirty-nine of these acres also count towards the 

SWRCB’s D-1641 requirements. 

Other Activities – The HRP provided funds for a 

Metcalf Canyon jewelflower captive propagation 

and reintroduction project in southern Santa Clara 

County. The objective is to reintroduce this federally 

endangered plant species at three sites on Tulare 

Hill, and to supplement an existing population at 

Motorcycle County Park. 

Year

Acreage 

Protected

Acreage 

Restored

Cumulative 

Acreage 

Progress of 

Protection 

and 

Restoration

1996 488 0 488

1997 149 743 1,380

1998 3,179 0 4,559

1999 497 0 5,056

2000 365 78 5,499

2001 559 0 6,058

2002 122 0 6,180

2003 459 0 6,639

2004 129 106 6,874

2005 58 727 7,659

2006 22 1,649 9,330

2007 16 51 9,397

2008 0 404 9,801

2009 2,050 13 11,864

2010 359 28 12,251

2011 930 139 13,320

2012 912 0 14,232

Total 10,294 3,938 14,232

Table 22: Acres of Habitat Protected and 

Restored by the (b)(1) “Other” Program, 1996-

2012, Using HRP Funds

Los Feliz Tract parcel. Project entails fee title acquisition of 

198 acres of grasslands habitat by the US Fish and Wildlife 

Service to expand the Pixley National Wildlife Refuge to 

benefit Tipton kangaroo rat, San Joaquin kit fox, and bluntnosed leopard lizard in Tulare County.
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 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 

89,000 acres, which 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 has reduced the production of agricultural 

drainage water by approximately 43,500 acrefeet through the removal of irrigation water from the 

parcels within the Land Retirement Demonstration 

Project from 1995-2012.

FY2012 ACCOMPLISHMENTS 

The program obligated $494,162 from the Restoration 

Fund, and $21,209 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 2012. Table 23 lists the 

cumulative accomplishments of land retirement and 

the annual restoration and ag drainage reduction 

accomplishments.

Restore Habitat – 9,500 pounds of locally grown 

seed from native plants were planted on three-hundred 

acres of previously acquired land at the Atwell Island

site in 2012. An excellent response of annual flora was 

observed at the restoration sites in the spring of FY 

2012, 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 4,100 acrefeet in FY 2012. 

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

2012 0 0 260 4,100

Total 7,266 2,090 6,671 43,563** 

 * 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 1995-2012.

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2012

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS 8

Central Valley Project Improvemen

CHAPTER 6

PROGRESS TO DATE

TOWARD CVPIA

ACCOMPLISHMENTS
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2012 

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 and 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 and 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 N/A N/A 39,000

Tons of Spawning gravel placed in the 

Mokelumne River

unspecified Annual N/A 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

Chapter 6 - Progress to Date 

Toward CVPIA Performance 

Goals

The CVPIA Program tracks performance targets from

several sources including CPAR (goals based upon 

CVPIA), Interior goals (Performance Assessment an

Rating Tool or PART) and program-defined goals. 

Listed below are goals by program for ongoing 

programs. The 2012 Accomplishment status is 

based upon the specific FY 2012 actions, cumulative 

Program to Date accomplishments, or a yearly 

average over the life of the program. At the bottom 

of the listing are completed or inactive programs and 

their status. Detailed assessments of progress toward 

the Central Valley fish doubling goals are found in 

the CAMP Annual Report at: http://www.fws.gov/

sacramento/fisheries/CAMP-Program/DocumentsReports/fisheries_camp-program_documents-reports.

htm. 
CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS 8

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2012 

Accomplishments Comments

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 N/A 100 800,000 2012 Water Year was classified 

Below Normal

WATER ACQUISITION - INSTREAM, 3406 (b)(3)

Provide supplemental (b)(2) instream flow 

water

200,000 acre-feet Average 

from 1994 - 

2012

78,576 40 38,500 FY2012 acquired water is 13% 

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

RED BLUFF DIVERSION DAM, 3406 (b)(10)

Increase the Fish Passage Rate of Adult 

Spring-run Chinook

80-100% Annual 100% 100 80% Within target range

Dam gates no longer operated

Increase the Fish Passage Rate of Adult 

Green Sturgeon

50-100% Annual 100% 100 75% Within target range

Dam gates no longer operated

Complete the fish screen and pumping 

plant

100% Cumulative 90% 90 25%

CLEAR CREEK RESTORATION, 3406 (b)(12)

Restore stream channel 2 miles Cumulative 1.5 75 0.0

Place spawning gravel annually 25,000 cy (1) Annual N/A 40 10,000

Meet variable flow target Annual 100 200 Ongoing operation

Maintain water temperature for optimum 

anadromous fish production

Maintain proper 

temperature 

100% of the time

Annual N/A 88 60°F 1-Jun to 14-Sep

56°F 15-Sep to 31-Oct

2011 data

SPAWNING GRAVEL, 3406 (b)(13)

Place 10,000 tons of spawning gravel 

annually in the Sacramento River.

10,000 tons Annual N/A 150 15,000

Place 3,000 tons of spawning gravel 

annually in the Stanislaus River

3,000 tons Annual N/A 100 3,000

Place 7,000 tons of spawning gravel 

annually in the American River

7,000 tons Annual 350 24,510

Increase the percentage of spawning 

salmonids using placed gravel in the 

Sacramento River

25% usage Annual N/A 24% 6% 

Increase the percentage of spawning 

salmonids using placed gravel in the 

Stanislaus River

10% usage Annual N/A 210% 21%

Increase the density of redds on emplaced 

gravel in the American River

0.03 redds/sq. 

meter

Annual 33 0.01

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 35 Undefined 2

TRINITY RIVER RESTORATION PROGRAM (TRRP), 3406 (b)(23)

Increase the escapment of Hatchery 

produced Fall-run Chinook Salmon

9,000 fish 1992 - 2012 

Average

19,175 194 17,461

Increase the escapment of Naturally 

produced Fall-run Chinook Salmon

62,000 fish 1992 - 2012 

Average

16,110 85 52,687

Increase the escapment of Hatchery 

produced Spring-run Chinook Salmon

3,000 fish 1992 - 2012 

Average

8,918 224 6,712

Increase the escapment of Naturally 

produced Spring-run Chinook Salmon

6,00 fish 1992 - 2012 

Average

6,079 296 17,730
84 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2012 

Accomplishments Comments

Increase the escapment of Hatchery 

produced Coho Salmon

2,100 fish 1992 - 2012 

Average

11,566 350 7,356

Increase the escapment of Naturally 

produced Coho Salmon

1,400 fish 1992 - 2012 

Average

1,890 567 7,939

Increase the escapment of Hatchery 

produced Steelhead

10,000 fish 1992 - 2012 

Average

12,347 57 5,737

Increase the escapment of Naturally 

produced Steelhead

40,000 fish 1992 - 2012 

Average

4,851 37 14,666

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

647,000 Annual N/A 100 647,000 Based on 2012 as a 

normal 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 28 60 4

Place 10,000 cubic yards of coarse 

sediment annually

10,000 cubic 

yards

Annual N/A 0 0

Reduce fine sediment delivery from 

tributary watersheds

10,000 to 20,000 

cubic yards

Annual N/A 150-300 30,000

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 13 of 15 87 2.6 MAF

Maintain minimum reservoir storage in 

Trinity Reservoir

600 TAF Cumulative 15 of 15 100 1,800 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 N/A 95 402,454

REFUGE WATER SUPPLY PROGRAM - CONVEYANCE, 3406 (d)(2)

Provide incremental Level 4 water supplies 133,264 

acre-feet

Annual N/A 42 55,515

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

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 0
CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS 8

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2012 

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 14,232 TBD 912 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 8,098 19 939

LAND RETIREMENT, 3408(h)

Retire 8,000 acres of Atwell Island land 8,000 acres Cumulative, 

1995–2012

7,266 91 0

Retire 7,000 acres of Tranquility land Complete Cumulative, 

1995–2012

7,000 100 N/A

Restore 400 acres of retired land annually 400 acres Cumulative, 

1995–2012

6,671 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, 

1995–2012

43,559 67 104

(1) Clear Creek spawning gravel replenishment goal was erroneously reported in the Final CPAR, 2009 as 17,000 tons annually. This unit of measure for this goal 

should have been cubic yards. Applying a conversion factor, 17,000 cubic yards of spawning gravel equates to approximately 25,000 tons. This correction first 

occurred in the 2012 Accomplishment Report and therefore, the percentage of annual goal for this year forward will appear smaller than past years of the same 

amounts of gravel.

COMPLETE AND INACTIVE PROGRAMS

Program Name Status

Modify CVP Operations, 3406 (b)(1)(B) Incorporated into various programs

Contra Costa Canal Pumping Plant, 3406 (b)(5) Complete

Shasta Temperature Control Device, 3406 (b)(6) Complete

Meet Flow Standards and Objectives, 3406 (b)(7) Complete

Short Pulse Flows, 3406 (b)(8) Incorporated into various programs

Coleman National Fish Hatchery, 3406 (b)(11) Complete

Delta Cross Channel and Georgiana Slough, 3406 (b)(14) Inactive

Head of Old River Barrier, 3406 (b)(15) Inactive

ACID Diversion Dam, 3406 (b)(17) Complete

Glenn-Colusa Irrigation District Program, 3406 (b)(20) Complete

Waterfowl Incentive Program, 3406 (b)(22) Complete

Trinity River Restoration Program, 3406 (b)(23) Complete

San Joaquin River Restoration Program, 3406 (c)(1) Complete. Currently funded through Public Law 111-11

Stanislaus River Basin Water Needs Program, 3406 (c)(2) Complete

Central Valley Wetlands Supply, 3406 (d)(6) Complete

Supporting Investigations, 3406 (e) Complete

Project Fisheries Impact Report, 3406 (f) Complete

Water Conservation Program, 3408 (i) Complete

Water Augmentation (Yield Study), 3408 (j) Complete

APPENDICES 8

Central Valley Project Improvemen

APPENDICES
88 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

AF acre-feet 

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program

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

CDFW California Department of Fish and Wildlife 

CPAR CVPIA Program Activity Review Repor

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 

FWA Friant Water Authority

FY Fiscal year

GCID Glenn-Colusa Irrigation Distri

GWD Grassland Water District

HGS HydroGeoSphere

HRP Habitat Restoration Program

IFIM Instream Flow Incremental Method

Interior Department of the Interi

IP Implementation P

IRWMT Interagency Refuge Water Managem

Team

LRP Land Retirement Program

NMFS National Marine Fisheries Service 

NOAA National Oceanic & Atmospheric

Administration

NRDC Natural Resources Defense Council

NWR National Wildlife Refuge 

OCAP Operations Criteria and Plan

OMB Office of Management and Budget 

PART Program Assessment Rating Tool

PEIS Programmatic Environmental Impa

Statement

POD Pelagic Organism Decline

RBDD Red Bluff Diversion Dam

RHEM Riparian Habitat Establishment Model

ROD Record of Decision

RPA Reasonable and Prudent Alternative

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 Refuge

SWP State Water Project

TFCF Tracy Fish Collection Facility 

TRRP Trinity River Restoration Program

Appendix A: Acronyms
APPENDIX B: 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 

Francisco Bay/Sacramento-San Joaquin 

Delta Estuary 

Appendix B: Glossary of Terms
90 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

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 

occurring water course (e.g., caught in a water 

pump or diverted from the river into an irrigation 

channel)

• 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 

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”
APPENDIX B: GLOSSARY OF TERMS 9

• 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 

oversee 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

• Replacement Water

CVP Water that was provided to five refuges 

prior to CVPIA. It is to be replaced to the Projec

when available and acquired from willing sellers. 

Replacement water is delivered in addition to the 

Level 2 amounts specified in the CVPI

• 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 of Delta

The area that includes the State Water 

Project authorized place of use downstream 

of Harvey O. Banks Pumping Plant and the 

Central Valley Project authorized place of use 

downstream of Jones Pumping Plant

• 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 runs from October 1-September 30
92 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Appendix C: 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.”
APPENDIX C: CVPIA TITLE 34 OF PUBLIC LAW 102-  

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 

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 
94 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

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...”

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;
APPENDIX C: CVPIA TITLE 34 OF PUBLIC LAW 102-  

(3) surface-ground and stream-wetland interactions;

(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.”
96 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

Appendix D: Maps

Central Valley Project (CVP) Service Area Boundary
APPEND

IX D: MAPS 9

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APPEND

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2012 CVPIA Accomplishments - Battle Creek Watershed
100 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

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APPEND

IX D: MAPS 10

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Mill Creek

Sacramento River

Thomes Creek

2012 CVPIA Accomplishments - Sacramento River, Lower Thomes, Mill Creek Watershed
APPEND

IX D: MAPS 10

2012 CVPIA Accomplishments - Deer Creek Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - D e e r C r e e k W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - D e e r C r e e k W a t e r s h e d

P:\CVPIA

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ProgramMgmt\Diane\2012 AR\maps_AR2012\DeerCreek_AR2012.mxd 0 4 8 12 16 2

Miles / . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Deer Creek

Sacramento River
104 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - Lower Feather River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r F e a t h e r R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r F e a t h e r R i v e r W a t e r s h e d

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ProgramMgmt\Diane\2012 AR\maps_AR2012\LowerFeatherRiver_AR2012.mxd

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Sacramento River
APPEND

IX D: MAPS 10

2012 CVPIA Accomplishments - Bear River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - B e a r R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - B e a r R i v e r W a t e r s h e d

P:\CVPIA

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Feather River . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Bear River Dry Creek
106 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - Bear River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - U p p e r S a c r a m e n t o R i v e r M a i n s t e m W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - U p p e r S a c r a m e n t o R i v e r M a i n s t e m W a t e r s h e d

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Sacramento River . Servic eLay erC edits: ©20 10NA VTE Q©2 013M icros oftC orp ation Servic eLay erC edits: ©20 10NA VTE Q©2 013M icros oftC orp

C

ation

onstruction two wells at Pixley NWR to provide for full

L2 water supplies and three wells at Gray Lodge WA to

provide a portion of this refuge's L2 supplies.
APPEND

IX D: MAPS 10

2012 CVPIA Accomplishments - Yuba River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - Y u b a R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - Y u b a R i v e r W a t e r s h e d

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Feather River . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Yuba River
108 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - American River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - A m e r i c a n R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - A m e r i c a n R i v e r W a t e r s h e d

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P:\CVPIA

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American River
APPEND

IX D: MAPS 10

2012 CVPIA Accomplishments - Lower Sacramento River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r S a c r a m e n t o R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r S a c r a m e n t o R i v e r W a t e r s h e d

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Sacramento River

Servic eLay erC edits: ©20 10NA VTE Q©2 013M icros oftC orp ation

Cosumnes River
110 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

2012 CVPIA Accomplishments - Coyote Creek Watershed

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Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n

Coyote Creek
APPEND

IX D: MAPS 11

2012 CVPIA Accomplishments - Lower Cosumnes & Mokelumne Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s 2 0 1 2 C V P I A A c c o m p l i s h m e n t s L o w e r C o s u m n e s & M o k e l u m n e R i v e r W a t e r s h e d L o w e r C o s u m n e s & M o k e l u m n e R i v e r W a t e r s h e d

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ProgramMgmt\Diane\2012 AR\maps_AR2012\LowerCosumnes_AR2012.mxd

0 6 12 18 24 3

Miles / . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n San Joaquin River

Cosumnes River

Mokelumne River
112 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

2012 CVPIA Accomplishments - San Joaquin River - Delta Watershed

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San Joaquin River

.

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Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n
APPEND

IX D: MAPS 11

2012 CVPIA Accomplishments - Lower Calaveras River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r C a l a v e r a s R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - L o w e r C a l a v e r a s R i v e r W a t e r s h e d

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Miles / . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n San Joaquin River

Calaveras River
114 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - Lower Stanislaus River Watershed 2 0 1 3 C V P I A A c c o m p l i s h m e n t s - L o w e r S t a n i s l a u s R i v e r W a t e r s h e d 2 0 1 3 C V P I A A c c o m p l i s h m e n t s - L o w e r S t a n i s l a u s R i v e r W a t e r s h e d

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San Joaquin River . Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n Servic eLay erC edits: ©20 10NA VTE Q©A ND© 2013 Micr osft Corp orati n

Stanislaus River

Restore 2.47 acres of riparian floodplain, create 0.7 acres of new floodplain, add 12,500

cubic yards of clean spawning gravel to the river, and restore 485 feet of side-channel

habitat to increase juvenile salmonid rearing habitat and decrease predation.

Restore 640 feet of riparian side channel habitat. Substantial post-project

assessments were conducted at the Lancaster Road project site, including

both physical and biological monitoring to evaluate project effectiveness.
APPENDIX D: MAPS 11

2012 CVPIA Accomplishments - Middle San Joaquin River - Lower Merced Watershed

2

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San Joaquin River

Tuolumne River

Merced

River
116 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - Tulare - Buena Vista Lakes Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - T u l a r e - B u e n a V i s t a L a k e s W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - T u l a r e - B u e n a V i s t a L a k e s W a t e r s h e d

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ProgramMgmt\Diane\2012 AR\maps_AR2012\TulareBVLakes_AR2012.mxd 0 10 20 30 40 5

Miles / . Servic eLay erC edits: ©20 10NA VTE Q©2 013M icros oftC orp ation Servic eLay erC edits: ©20 10NA VTE Q©2 013M icros oftC orp ation Construction of two wells at Pixley NWR to provide for full L2 water supplies and three wells at Gray Lodge WA to provide a portion of this refuge's L2 supplies.
APPENDIX D: MAPS 11

2012 CVPIA Accomplishments - Middle San Joaquin River - Lower Chowchilla Watershed

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San Joaquin River

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Bear Creek

Fee title acquisition of 240 contiguous acres of land

to complete the protection of lands surrounding the

confluence of Silver Creek & Panoche Creek (Lower

Silver Creek) in Fresno County. Species to benefit

include San Joaquin kit fox, giant kangaroo rat, and

San Joaquin woolly-threads.

San Joaquin River
118 CENTRAL VALLEY PROJECT 

IMPROVEMENT ACT – ISCAL YEAR 2012 ANNUAL REPOR

2012 CVPIA Accomplishments - Upper Los Gatos Creek Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - U p p e r L o s G a t o s C r e e k W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - U p p e r L o s G a t o s C r e e k W a t e r s h e d

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Los Gatos Creek

Salinas River
APPEND

IX D: MAPS 11

2012 CVPIA Accomplishments - Salinas River Watershed 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - S a l i n a s R i v e r W a t e r s h e d 2 0 1 2 C V P I A A c c o m p l i s h m e n t s - S a l i n a s R i v e r W a t e r s h e d

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Construct four new groundwater production wells GRCD. One half of the water from these

groundwater production wells will provide IL4 water supplies to GRCD,state, and federal

CVPIA refuges on the west side of the San Joaquin Valley and the rest will help

diversify refuge L2 water supplies in accordance with CVPIA.
120 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPO

2012 CVPIA Accomplishments - Carrizo Plain Watershed

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Cuyama River