U.S. Department of the Interior

Bureau of Reclamation 

U.S. Fish and Wildlife Service January 2014

Central Valley Project 

Improvement Act

Public Law 102-575

Annual Report

Fiscal Year 2013
Cover photographs:

Top: Trinity River. Restoration projects create new fish habitat by increasing bank length. 

A straight channel, once restricted by the large trees seen in the middle of the new island, is 

now divided into two channels that each carry 50% of the flow - still allowing boating and 

fishing. Note the large wood structure that helps direct flows and also provides additional 

fish habitat by mimicking the natural processes that once maintained anadromous fish 

habitat in free flowing rivers. 

Middle: White-faced Ibis on nest at Kern National Wildlife Refuge.

Bottom: Juvenile steelhead/rainbow trout in a favored feeding location in the Stanislaus 

River.
TABLE OF CONTENTS 

Central Valley Project Improvemen

Table of Contents
i    CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL RE

Table of Contents

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

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

CHAPTER 2 - FISHERIES RESOURCE AREA........................................................................................................11

3406 (b)(1) Anadromous Fish Restoration Program............................................................................................12

3406 (b)(1) Bay-Delta Activities ...........................................................................................................................24

3406 (b)(1) “Other” & (b)(23) Trinity River Restoration Program .........................................................................25

3406 (b)(4) Tracy (Jones) Pumping Plant Program............................................................................................29

3406 (b)(12) Clear Creek Restoration Program...................................................................................................31

3406 (b)(13) Spawning and Rearing Habitat Restoration Program.....................................................................35

3406 (b)(16) Comprehensive Assessment and Monitoring Program...................................................................38

3406 (b)(21) Anadromous Fish Screen Program.................................................................................................41

Public Law 111-11 San Joaquin River Restoration Program ...............................................................................43

3406 (g) Ecosystem and Water Systems Operations Models .............................................................................45

CHAPTER 3 - CVP WATER OPERATIONS RESOURCE AREA.............................................................................47

3406 (b)(2) Dedicated 800,000 acre-feet Project Yield........................................................................................48

3406 (b)(3) Water Acquisition Program – Instream Water...................................................................................51

3406 (b)(9) & (b)(19) Flow Fluctuations and Reservoir Storage..........................................................................53

3404 (c) & 3405 Contract Renewals and Water Transfers ..................................................................................55

CHAPTER 4 - REFUGES RESOURCE AREA .........................................................................................................57

3406 (d)(1), (2) & (5) Refuge Water Supply Program..........................................................................................58

3406 (d)(2) Refuge Water Acquisition..................................................................................................................61

3406 (d)(1), (2) & (5) Refuge Water Conveyance................................................................................................63

3406 (d)(5) Refuge Facilities Construction Component.......................................................................................66

CHAPTER 5 - OTHER RESOURCE AREA..............................................................................................................69

3406 (b)(1) “Other” Habitat Restoration Program................................................................................................70

3408 (h) Land Retirement Program.....................................................................................................................72

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS ..............................................76

APPENDIX A: ACRONYMS.....................................................................................................................................82

APPENDIX B: GLOSSARY OF TERMS..................................................................................................................83

APPENDIX C: CVPIA TITLE 34 OF PUBLIC LAW 102-575...................................................................................86

APPENDIX D: MAPS...............................................................................................................................................89

LIST OF FIGURES

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

Figure ES-2: FY 2013 Financial Obligations By Action Category (in $ millions)...........................................ES-11

Figure ES-3: FY 2013 Financial Obligations By Fund Source (in $ millions)......................................................11

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

Figure 2: Program Financial Obligations By Action Category to Date (in $ millions)............................................7

Figure 3: Program Financial Obligations By Fund Source to Date (in $ millions).................................................7

Figure 4: FY 2013 Financial Obligations By Action Category (in $ millions).........................................................8

Figure 5: FY 2013 Financial Obligations By Fund Source (in $ millions)..............................................................8
TABLE OF CONTENTS 

LIST OF TABLES

Table ES-1: FY 2013 Breakdown of Funding Obligations by Program Activity ............................................ES-10

Table 1: FY 2013 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, 1992-2012.................................13

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

 Evaluations by Watershed, FY 1992-2013 .....................................................................................14

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

 (53 Structural, 75 Non-Structural) ..................................................................................................15

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

 Doubling Goal Targets, 1992-2012.................................................................................................16

Table 6: FY 2012 Salmonid Production, Natural vs. Hatchery1 ...................................................................26

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2013..............................................27

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2013 ................................28

Table 9: Rehabilitation Site Construction Summary, 2005-2013 .................................................................28

Table 10: Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan Actions ..........30

Table 11: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2013..................................37

Table 12: AFSP Projects by Watershed and Cubic Feet per Second (cfs) Screened, 1994-2013.................42

Table 13: Ecosystem and Water System Operations Models Developed To Date.........................................46

Table 14: Allocation Target and Use of (b)(2) Water, 2001-2013....................................................................49

Table 15: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 1994-2013...........52

Table 16: Carryover Storage at Shasta and Trinity Reservoirs, 1998-2013 ...................................................54

Table 17: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2013..........................................................62

Table 18: Level 2 (L2), Incremental Level 4 (Inc L4) and Full Level 4 Delivery Water by Year, 2002-2013 ...64

Table 19: Water Targets and Deliveries for Each Refuge (FY 2013)..............................................................65

Table 20: Target FL4 Conveyance Capacity vs. Actual by Refuge.................................................................68

Table 21: Approximate Acres of Habitat Protected and Restored by the (b)(1) “Other” Program, 

 1996-2013, using HRP Funds ........................................................................................................71

Table 22: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2013 .................................73

EXECUTIVE SUMMARY ES-1

Central Valley Project Improvemen

Executive Summary
ES-2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

PURPOSE

This fiscal year (FY) 2013 CVPIA Annual 

Accomplishments Report summarizes the actions 

and accomplishments authorized under the Central 

Valley Project Improvement Act (CVPIA or Act) of 

1992 for October 1, 2012 - September 30, 2013. 

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, 2013 

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. 

Title 34 of the law 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, nongovernmental 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. 

CVPIA Goals and FY 2013 

Accomplishments 

The current focus of the CVPIA Program is on fish 

and wildlife restoration, water management, and 

Executive Summary

Tule elk at San Luis NWR.
EXECUTIVE SUMMARY ES-3

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 highlights of 2013 accomplishments. 

Chapters 2, 3, 4 and 5 of this report provide 

information on the accomplishments of each resource 

area, while a synopsis of the programs targets, status 

to date and 2013 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 

Preparing a juvenile salmon with a hydro-acoustic tag for the Whole Facility Evaluation Study, Tracy Fish Collection Facility 
ES-4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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. 

2013 Accomplishments

Anadromous Fish Restoration Program 

(AFRP), 3406 (b)(1)

The Final AFRP Restoration Plan calls for addressing 

the limiting factors in each watershed. On watersheds 

where the CVPIA substantially addressed most 

limiting factors, fish populations have exceeded the 

doubling goals. These watersheds include Clear 

Creek, Butte Creek, and Battle Creek. The AFRP 

continued progress toward actions and evaluations 

in the Sacramento and San Joaquin watersheds to 

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)(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)(10) Red Bluff Diversion Dam

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)

* In FY 2012, the Red Bluff Diversion Dam Program substantially completed construction of the new, 2,500-cfs permanent pumping plant and fish 

screen. Fine tuning of the pumping plant equipment and monitoring of the riparian mitigation site continues to occur using non-CVPIA Restoration Funds.
EXECUTIVE SUMMARY ES-5

enhance passage and habitat, and reduce loss of fish. 

About 23% of the 289 Restoration Plan actions and 

evaluations have been completed to date. Of the 

128 “time certain” high and medium priority actions, 

forty-six (36%) have been completed. Although no 

structural or non-structural actions were completed 

in FY 2013, various projects to address high priority 

limiting factors in 20 watersheds continued, including 

fish passage, entrainment, habitat restoration, and 

spawning gravel augmentation projects as well 

as variety of assessments and evaluations that are 

providing information critical for future projects. The 

most recent fish count data is presented through 2012.

Dedicated 800,000 acre-feet (AF) Project 

Yield, 3406 (b)(2)

700,000 AF of (b)(2) water was available for 

fish actions in water year 2013 consistent with the 

shortage provisions in the Act for dry years. 

Water Acquisition Program – Instream 

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

Up to 25,000 acre feet of supplemental water was 

made available to help meet the Vernalis spring 

flow target. Flows were not required in 2013 to meet 

targets, therefore, the acquisition was not exercised.

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

Actions taken to improve the Tracy Fish Facility in FY 

2103 include continued work to improve the louver 

systems, the development of land for onsite research 

and fish protection, replacement of the secondary 

louvers, the continued work towards a third fish 

release site and various research studies that will 

improve fish capture and reintroduction capabilities.

Clear Creek Restoration Program (CCRP), 

3406 (b)(12) 

The CCRP provided instream pulse flows and 

maintained temperature of flows to attract fish and 

promote upstream movement. The program also 

evaluated past spawning gravel placement and 

monitored the impacts of the 2008, 2012 and 2013 

wildfires in the South Fork Clear Creek tributary. The 

program continued monitoring fish populations with 

2012 escapement numbers for full-run estimated at 

7,631.

Cottonwood and willow pole cuttings being planted with a “stinger” implement mounted on a backhoe as part of the Hammon Bar 

riparian restoration pilot project, lower Yuba River, California.
ES-6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Spawning and Rearing Habitat 

Restoration Program, 3406 (b)(13)

In 2013, the program placed 14,000 tons of gravel 

just below Keswick Dam on the Sacramento River 

and placed 6,000 tons of gravel and improved a 

400-yard long side channel at River Bend Park on the 

American River. The program conducted monitoring 

of redd surveys and surveys of downstream movement 

of previously placed gravel on the Stanislaus River. 

Comprehensive Assessment and 

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

CAMP produced its 2012 annual report assessing the 

overall effectiveness of actions implemented pursuant 

to CVPIA section 3406(b) in meeting AFRP fish 

production targets. CAMP continues to support fish 

population evaluations through the development of 

the Rotary Screw Trap Platform, monitoring at several 

locales within the CVP area, marking and tagging 

of juvenile fall-run Chinook salmon at the Nimbus 

Fish Hatchery and Coleman National Fish Hatchery 

and studies on the Cottonwood and Battle Creeks. 

The program also supported the Science Based 

Management Framework in conjunction with the other 

fisheries programs to develop tools and a process that 

will enable a comprehensive and prioritized fisheries 

management approach CVPIA-wide.

Anadromous Fish Screen Program 

(AFSP), 3406 (b)(21) 

Construction was completed on 6 new fish screens 

including the Natomas Mutual Sankey Fish Screen 

Project (389 cfs); River Garden Farms #3 -Townsite 

(62 cfs), Alamo Farms #1 (36 cfs), Tisdale Irrigation 

District #2 (44 cfs), and Cranmore Farms #2 (40 cfs) 

on the Sacramento River, and Joe Sanchez Farms 

(24 cfs) in the Sacramento-San Joaquin Delta. The 

AFSP continued to support the following fish screen 

projects: RD 2035/Woodland Davis Clean Water 

Agency Joint Intake, Lake Pritchard, and Colusa 

Indian Community Council on the Sacramento River; 

Feather Water District North and South diversions on 

the Feather River; South Sutter #1 on Auburn Ravine, 

and West Stanislaus Irrigation District on the lower 

San Joaquin River.

Ecosystem and Water Systems Operation 

Models, 3406 (g) 

The Modeling Program continued to develop models 

and supporting data to evaluate water management 

strategies for the CVPIA Programs. In FY 2013, 

the program continued ongoing development and 

modification of the following programs: CalSim II, 

the CalLite, CalSim 3.0, HEC-5Q based temperature 

model, C2VSIM (California Central Valley 

Groundwater-Surface Water Simulation Model), 

ANN, DSM2, inSALMO, and HydroGeoSphere 

(HGS). The program also prepared publications and 

provided support to model applications. 

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 (EIS/

EIR).

In 2013, the TRRP placed gravel at the Lewiston 

Diversion Pool during the 4,500 cfs peak flow (200 

cubic yards (CY)) and at Sawmill rehabilitation 

site (1,500 CY). Channel rehabilitation projects 

were implemented at 2 sites on Lorenz Gulch. Five 

watershed projects including watershed condition 

assessments and educational outreach activities 

were completed in FY 2013 that kept approximately 

15,500 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.
EXECUTIVE SUMMARY ES-7

San Joaquin River Basin

San Joaquin River Restoration Program, 

P.L. 111-11 

Section 10009 (b)(2) of Public Law 111-11 authorizes 

up to $2 million (indexed to 2006 funds) from the 

CVP Restoration Fund for implementation of the 

San Joaquin River Restoration Program (SJRRP). 

Activities, including planning and environmental 

studies aim 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 long-term 

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 Central Valley Project Restoration Fund 

supplements the program’s funding under PL 111-11.

In FY 2013, the SJRRP coordinated technical 

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 Program 

continued the environmental analysis for the Reach 

4B and Mendota Pool Bypass projects, as well as the 

Conservation Facility development. The Program also 

established the broodstock population of spring-run 

Chinook salmon at the Interim Conservation Facility.

CVP Water Operations Resource Area 

Goals

The CVPIA includes several programs 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; and 3406 (b)(9)/(b)(19), Flow 

Fluctuations and Reservoir Storage. Two ongoing 

programs, Flow Standards and Objectives and Short 

Pulse Flows are incorporated into the operations of 

overarching programs such as Clear Creek and Flow 

Fluctuations.

The Modified CVP Operations Program determines 

the instream flow needs in CVP streams by Instream 

Flow Incremental Methodology (IFIM) studies that 

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 project 

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.

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 

three salmonid isolation pool surveys and multiple 

steelhead redd surveys on the American River. The 

Sacramento River Stranding Project, a collaborative 

project with Golden Gate Salmon Association, 

began in FY 2013 to reduce fall chinook salmon 

redd dewatering post-irrigation season. Additionally, 

a Flow Fluctuation Study was completed on the 

Stanislaus River. The RSP met the carryover targets for 

Shasta and Trinity reservoirs with 1.9 million acre feet 

(AF) and 1,303 thousand AF, respectively. 

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. Full 

Level 4 water is the sum of Level 2 and Incremental 

Level 4 water.
ES-8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Water Acquisitions – Refuge Water 

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

In 2013, the RWAP purchased up to 40,596 AF 

of water for Water Year 2013 through contracts 

with Grasslands Water District, San Joaquin River 

Exchange Contractors Water Authority and Merced 

Irrigation District.

Refuge Water Conveyance Component 

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

The RWCC delivered an estimated 389,343 AF of 

Level 2 water and an estimated total of 48,096 AF 

of Incremental Level 4 water to the refuges during FY 

2013. Of the Level 2 water, a total of 51,879 AF was 

delivered from diverse, non-CVP sources.

Reclamation delivered 100 percent of Level 2 water 

supplies scheduled by CVPIA refuges in FY 2013. 

The goal of delivering 422 TAF was not met for 

several reasons. Contributing factors to refuges not 

scheduling 100% of their L-2 allocation include:

•	Conveyance capacity restrictions to certain 

refuges;

•	Refuge internal distribution systems groundwater 

pump mechanical failures;

•	Unexpected erosion around newly constructed 

alfalfa valves;

•	Regionally, a few refuges received more 

precipitation than other refuges, reducing their 

demand for full Level 2 during certain months in 

FY2013; and

•	Water schedules that are developed and 

implemented on a water-year basis versus a 

fiscal-year. Much of the RWSP is implemented 

and operated on a water-year basis, including 

the Refuge Water Supply Contracts and refuge 

water conveyance agreements. 

Refuge Facilities Construction 

Component (RFCC), 3406 (d)(5)

To date, 15 of the 19 CVPIA refuges have the external 

conveyance capacity to receive Full Level 4 water. 

In FY 2013, the RFCC focused construction efforts 

at the East Bear Pumping Plant located at the East 

Bear Creek Unit of the San Luis National Wildlife 

Refuge Complex, and at the Gray Lodge and Pixley 

groundwater wells. Initial studies began to assess 

a water supply conveyance system for the Sutter 

National Wildlife Refuge and for the final design of 

the Biggs-West Gridley Water District (BWGWD) 

Facilities Improvement Project.

Other Resources Area Goals

The fourth focus of the CVPIA restoration initiatives 

is directed at terrestrial habitat and species; water 

quality and conservation; and contract renewals and 

transfers. Provisions supporting this initiative include 

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

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

Program (LRP); and Sections 3404 and 3405, 

Contract Renewals and Water Transfers. 

Habitat Restoration Program (HRP), 3406 

(b)(1) “Other”

The HRP focuses on protecting and restoring 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 through restoring lands to native 

habitat. The HRP also funds research, and captive 

propagation and reintroduction projects. The HRP 

contributes to the protection and/or restoration 

of the 2.7 million acres of habitat affected by the 

construction and operation of the CVP. The 1999 

State Water Resources Control Board Decision 1641 

(SWRCB’s D-1641) requires that Reclamation provide 

compensation and habitat values to mitigate for 

impacts associated with the delivery of CVP water 

to lands previously outside the CVP Consolidated 

Place of Use. It identifies the HRP as one of three 

Reclamation programs suitable for fulfilling the 

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

Reclamation developed the Consolidated Place of 

Use, Habitat Mitigation Plan and Monitoring and 

Reporting Program (HMP) as a report/strategy of 

how the mitigation requirements will be addressed. 

The HMP identifies acquisition, maintenance, and 

restoration of 45,391 acres needing to occur as 

mitigation related to the CVP Consolidated Place of 

Use. To date, the program has protected 954 acres 

of land towards the D-1641 goal.

In 2013, the HRP helped protect 1,953 acres of land 

through fee title acquisitions in Fresno, Butte and 

Tulare Counties. The HRP also provided funds for 
EXECUTIVE SUMMARY ES-9

genetic research for the endangered riparian brush 

rabbit in San Joaquin 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 2013, the LRP planted 5,900 pounds of locally 

grown seed from native plants on 197 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 3,600 AF in 

FY 2013. 

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 to 

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, 100 long term renewal contracts and 28 

interim-renewal contracts have been executed within 

the various divisions of the CVP. 132 long term 

contracts have been renewed with the Sacramento 

River Water Right Settlement contractors and 1 is 

pending renewal upon expiration in July 2020. 

Reclamation approved the transfer of 472,393 acrefeet of CVP water for transfer for FY 2013. 

FUNDING 

For FY 2013, $50.4 million was appropriated to the 

Restoration Fund. As shown in Figures ES-3, a total 

of $88.0 million was obligated on CVPIA projects 

from a combination of funding sources: Restoration 

Funds ($53.8 million), Water and Related Resources 

($24.8 million), state cost share funds ($0.1 million), 

and Bay-Delta funds ($9.8 million). See Table ES-1 

for a breakdown of funding for each CVPIA Program 

activity in FY 2013.

In 2013, 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. The Gravel Placement Task 

Order was completed in FY 2013. The remaining Task 

Orders and Amendment No. 7 are expected to be 

in place by the end of FY 2014. FY 2015 will require 

negotiations of a new cost share agreement.

RECENT DEVELOPMENTS 

Refuges 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. 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 (http://www.

usbr.gov/mp/cvpia/docs_reports/index.html). 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, 
ES-10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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

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 Fisheries Program” dated 

December 2008) http://www.usbr.gov/mp/cvpia/

docs_reports/index.html), which calls for a sciencebased adaptive management approach, increased 

focus on the Bay-Delta and increased flows for fish. 

It is expected that the entire decision making 

process with system-wide model, objectives and a 

recommendation for a supporting organizational 

structure will be presented for public feedback for 

implementation in 2015. 

Operations Criteria and Plan (OCAP) 

And Biological Opinions in the Delta

In FY 2013, the CAMP Program contributed to 

meeting the RPA requirements through on the ground 

activities. Examples include the monitoring of juvenile 

Chinook salmon at various locales in the CVP Service 

Area Boundary. 

Table ES-1: FY 2013 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 0 430,184 0 430,184

3406(b)(1) Anadromous Fish Restoration Program 577,508 8,809,702 0 6,247,468 0 15,634,678

3406(b)(1) Habitat Restoration Program 0 1,604,246 0 0 0 1,604,246

3406(b)(1) Trinity River Restoration Program 10,782,901 1,999,143 0 0 0 12,780,044

3406(b)(23) Trinity River Restoration 3,214,440 0 0 0 0 3,214,440

3406(b)(2) Dedicated Project Yield 0 551,887 0 0 0 551,887

3406(b)(3) Water Acquisition Program - 

Instream Water

 2,565,077 2,940,055 0 0 0 5,505,132

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

Plant Program

Tracy (Jones) 

Pumping Plant1

 1,354,568 0 0 0 0 1,354,568

Two Gates 0 0 0 18 0 0

3406(b)(5) Contra Costa Pumping Plant No. 1 22,082 233,391 99,882 0 102,906 458,261

3406(b)(9) Flow Fluctuations 0 96,965 0 0 0 96,965

3406(b)(10) Red Bluff Diversion Dam 5,929,812 0 (27,610) 0 (625,071) 5,277,131

3406(b)(12) Clear Creek Restoration Program 0 612,992 0 0 0 612,992

3406(b)(13) Spawning Gravel 0 620,753 0 0 0 620,753

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 1,386,732 0 0 0 1,386,732

3406(b)(20) Glenn Colusa Irrigation District 351 0 0 0 0 351

3406(b)(21) Anadromous Fish Screen Program (63,258) 5,169,957 0 2,800,000 0 7,906,699

PL 111-11 San Joaquin River Restoration Program2 0 1,922,015 0 0 0 1,922,015

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

3406(d)(2) Refuge Water Supply Level 4 0 5,250,711 0 350,000 0 5,600,711

3406(d)(5) Refuge Facilities 

Construction Program

Construction 0 9,583,686 0 0 (3,875) 9,579,811

Wheeling 200,000 11,277,741 0 0 0 11,477,741

3406(d)(5) San Joaquin Basin Action Plan (1,436) 31,985 0 0 0 30,549

3406(g) Ecosystem & Water System Operations 

Models

 180,840 863,020 0 0 0 1,043,860

3408(h) Land Retirement Program 45,280 296,843 0 0 0 342,123

3410 CVPIA Administration 584 580,280 0 0 0 580,864

TOTAL FUNDING OBLIGATED 24,808,749 53,830,104 72,272 9,827,652 (526,040) 88,012,737

1

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

2

 Only represents funding from the CVPIA Restoration Fund.
EXECUTIVE SUMMARY ES-11

Figure ES-2: FY 2013 Financial Obligations By Action Category (in $ millions)

Figure ES-3: FY 2013 Financial Obligations By Fund Source (in $ millions)

Total Obligations: $88.0 Million

Total Obligations: $88.0 Million
ES-12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Sediment monitoring helps quantify sediment loads and adaptively manage future coarse sediment augmentation based on the 

transport rates and distance of different sizes of coarse gravel.
INTRODUCTION 1

Central Valley Project Improvemen

Chapter 1

Introduction
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

PURPOSE

This fiscal year (FY) 2013 CVPIA Annual 

Accomplishments Report summarizes the actions 

authorized under the Central Valley Project 

Improvement Act (CVPIA or Act) of 1992 and 

highlights FY 2013 accomplishments (October 1, 

2012 - September 30, 2013). 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. This reports describes the goals of the Act, 

CVPIA background, program funding and recent 

developments. Program performance measures, 2013 

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. 

BACKGROUND

Authorized in 1935, the CVP 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 water in the Central Valley originates in the north 

and is conveyed southward, primarily through the 

Sacramento River system (see Figure 1). The water 

then flows into the Sacramento-San Joaquin River 

Delta before it is either pumped south or discharged 

to the San Francisco Bay and the Pacific Ocean.

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 legislation amends 

previous authorizations of the California Central 

Valley Project (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 CVPIA addressed the importance of the CVP 

to the State’s water resources, and made significant 

changes in the policies and administration of the 

project. 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), partners, 

organizations and stakeholders during each fiscal 

year to plan and implement activities. 

Chapter 1 - Introduction
INTRODUCTION 3

Figure 1: Central Valley Project (CVP) System
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

For 75 years, Central and Southern California has 

relied on the CVP for a large part of its farm, urban 

and industrial water demands. The ecosystems of the 

Central Valley, Delta Estuary, San Francisco Bay, and 

Trinity River are affected by these 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 actions 

are in addition to and complement the mandates 

of the fish and wildlife protection, restoration and 

enhancement provisions of the Act. 

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. 

A synopsis of the programs targets, status to date and 

2013 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 uses 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 

Predator removal using CO2 at Tracy Fish Facility.
INTRODUCTION 5

State of California (State). The Act specifies whether 

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(d) of the CVPIA, 

is an account in the Treasury of the United States 

(U.S.) and consists largely of revenue generated by 

fees levied on CVP water and power users. The total 

maximum annual RF appropriation authorized by 

CVPIA is $50 million (1992 price levels). Of this, $30 

million (1992 price level) is the maximum amount 

(payment ceiling) that is authorized to be assessed 

and collected from the water and power users for 

mitigation and restoration payments specified in 

Section 3407(c)(2). The $30 million payment ceiling is 

calculated on a 3-year rolling average, which results 

in a cyclical funding pattern when collections are 

limited by the water deliveries and appropriations 

are limited by Congress. The annual appropriation 

bill from Congress provides budget authority based 

on estimated collections, and the obligation of these 

funds can only occur after the collections are made. 

Funding Obligations to Date

Since FY 1993, Congress appropriated RF and W&RR 

funds to the CVPIA Program. In addition, funds have 

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

funds and the American Recovery and Reinvestment 

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

total of $1.6 billion has been obligated by the CVPIA 

Program over the past 20 years, as shown in Figures 

2 and 3. 

FY 2013 

For FY 2013, $50.4 million was appropriated to 

the Restoration Fund. As shown in Figure 5, a total 

of $88.0 million was obligated on CVPIA projects 

from a combination of funding sources: Restoration 

Funds ($53.8 million), Water and Related Resources 

($24.8 million), state cost share funds ($0.1 million), 

and Bay-Delta funds ($9.8 million). See Table 1 for 

a breakdown of funding for each CVPIA Program 

activity in FY 2013.

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 amount 

payable was $50 million through the agreements 

expiration in December 31, 2008.

Amendment No. 1 to SCAMPI, executed in June 

1998, specified that the maximum amount payable 

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

was $93 million, the amount of funding provided 

by Proposition 204. Amendment No. 2 to SCAMPI, 

executed in August 2001, increased the maximum 

amount payable by the State pursuant to the 

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

Amendment No. 3 to SCAMPI, executed in December 

2008, resulted in an extension of SCAMPI for 

an additional three years to December 31, 2011. 

Amendment No. 4 to SCAMPI, executed in February 

2010, increased the maximum amount payable by the 

State pursuant to the cost-share provisions of CVPIA to 

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

Order. Amendment No. 5 to SCAMPI, executed in 

2011, increased the maximum amount payable to the 

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

Adaptive Management Plan (VAMP) Task Order 

Agreement. Amendment No. 6, also executed in 

2011, increased the maximum amount payable to the 

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

the Fish Passage Improvement Project at the Red Bluff 

Diversion Dam.

In 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. The Gravel Placement Task 

Order was completed in FY 2013. The remaining 

Task Orders and Amendment No. 7 are expected 

to be in place by the end of FY 2014. FY 2015 will 

require negotiations of a new cost share agreement.
6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Shasta Dam.
INTRODUCTION 7

Figure 2: Program Financial Obligations By Action Category to Date (in $ millions)

Figure 3: Program Financial Obligations By Fund Source to Date (in $ millions)

Total Obligations: $1,618 Million

Total Obligations: $1,618 Million
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Figure 4: FY 2013 Financial Obligations By Action Category (in $ millions)

Figure 5: FY 2013 Financial Obligations By Fund Source (in $ millions)

Total Obligations: $88.0 Million

Total Obligations: $88.0 Million
INTRODUCTION 9

Table 1: FY 2013 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 0 430,184 0 430,184

3406(b)(1) Anadromous Fish Restoration Program 577,508 8,809,702 0 6,247,468 0 15,634,678

3406(b)(1) Habitat Restoration Program 0 1,604,246 0 0 0 1,604,246

3406(b)(1) Trinity River Restoration Program 10,782,901 1,999,143 0 0 0 12,780,044

3406(b)(23) Trinity River Restoration 3,214,440 0 0 0 0 3,214,440

3406(b)(2) Dedicated Project Yield 0 551,887 0 0 0 551,887

3406(b)(3) Water Acquisition 

Program - Instream Water

 2,565,077 2,940,055 0 0 0 5,505,132

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

Plant Program

Tracy (Jones) 

Pumping Plant1

 1,354,568 0 0 0 0 1,354,568

Two Gates 0 0 0 18 0 0

3406(b)(5) Contra Costa Pumping Plant No. 1 22,082 233,391 99,882 0 102,906 458,261

3406(b)(9) Flow Fluctuations 0 96,965 0 0 0 96,965

3406(b)(10) Red Bluff Diversion Dam 5,929,812 0 (27,610) 0 (625,071) 5,277,131

3406(b)(12) Clear Creek Restoration Program 0 612,992 0 0 0 612,992

3406(b)(13) Spawning Gravel 0 620,753 0 0 0 620,753

3406(b)(16) Comprehensive Assessment and Monitoring 

Program

 0 1,386,732 0 0 0 1,386,732

3406(b)(20) Glenn Colusa Irrigation District 351 0 0 0 0 351

3406(b)(21) Anadromous Fish Screen Program (63,258) 5,169,957 0 2,800,000 0 7,906,699

PL 111-11 San Joaquin River Restoration Program2 0 1,922,015 0 0 0 1,922,015

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

3406(d)(2) Refuge Water Supply Level 4 0 5,250,711 0 350,000 0 5,600,711

3406(d)(5) Refuge Facilities 

Construction Program

Construction 0 9,583,686 0 0 (3,875) 9,579,811

Wheeling 200,000 11,277,741 0 0 0 11,477,741

3406(d)(5) San Joaquin Basin Action Plan (1,436) 31,985 0 0 0 30,549

3406(g) Ecosystem & Water System Operations 

Models

 180,840 863,020 0 0 0 1,043,860

3408(h) Land Retirement Program 45,280 296,843 0 0 0 342,123

3410 CVPIA Administration 584 580,280 0 0 0 580,864

TOTAL FUNDING OBLIGATED 24,808,749 53,830,104 72,272 9,827,652 (526,040) 88,012,737

1

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

2

 Only represents funding from the CVPIA Restoration Fund.
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Wildflowers: Valley Downingea in Grasslands Resource Conservation District.
Central Valley Project Improvemen

Chapter 2

FISHERIES

RESOURCE 

AREA
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

The Anadromous Fish Restoration Program (AFRP) is 

the overarching program to address anadromous fish 

doubling in the Central Valley. The Act specifically 

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...”

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 or eliminating 

entrainment of juveniles at diversions 

•	Improve the opportunity for adult fish to reach 

their spawning habitats in a timely manner 

•	Collect fish population, health, and habitat data 

to facilitate evaluation of restoration actions

•	Integrate habitat restoration efforts with harvest 

and hatchery management 

•	Involve partners in implementing and evaluating 

restoration actions

PERFORMANCE MEASURES

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.

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 fish-doubling 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 non-structural actions (75), 

such as flow fluctuations or studies (Table 4). 

FY 2013 ACCOMPLISHMENTS 

The AFRP obligated $8,809,702 from the Restoration 

Fund and $577,508 from the Water and Related Fund 

in FY 2013. 

Anadromous Fish Restoration 

Program

3406 (b)(1)
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 13

FISHERIES

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

 Production by Species within Central Valley River and Streams, 1992-2012

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 192,117 27,778 3,167 4,463

1993 5,153 656,505 68 692 316,846 2,411 1,060 4,229

1994 1,318 599,770 N/A 6,392 382,650 1,063 505 7,811

1995 6,803 N/A N/A N/A 709,299 764 4,284 36,884

1996 4,260 1,043,239 N/A N/A 485,160 453 2,160 6,309

1997 2,591 N/A 1,306 11,689 601,000 1,350 2,079 3,866

1998 4,134 1,356,412 470 8,971 272,337 83,027 5,680 49,676

1999 715 N/A N/A N/A 399,951 17,299 5,472 11,163

2000 764 1,591,419 N/A N/A 658,688 19,933 2,657 11,643

2001 761 N/A 7,117 5,129 525,947 27,679 9,916 31,185

2002 1,914 945,878 1,690 2,775 537,843 56,588 9,195 31,626

2003 9,342 829,111 N/A N/A 518,803 9,106 10,853 33,319

2004 947 1,312,452 N/A N/A 507,252 21,277 14,812 28,674

2005 1,741 1,058,679 2,555 2,898 395,601 20,738 21,417 38,813

2006 2,303 N/A 3,144 6,991 227,677 15,575 19,680 14,487

2007 551 752,275 1,530 10,559 106,592 30,326 4,121 16,777

2008 271 1,116,062 1,330 6,257 39,236 4,806 2,555 11,619

2009 624 830,641 10,272 6,258 30,604 4,350 4,070 3,196

2010 683 696,159 N/A N/A 120,464 5,860 1,534 3,222

2011 892 894,606 N/A N/A 170,321 5,645 899 6,847

2012 414 742,853 N/A N/A 293,985 5,539 3,900 30,522

Average

% of 

Goal

N/A

N/A

2,389

56%

 964,033

39%

 2,948

147%

 6,237

 57%

356,780

48%

17,218

25%

 6,191

 5.6%

 18,397

 27%

 

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

 2012.

c Estimated abundance of adult striped bass in the Central Valley’s anadromous waters, 1992-2012. Estimates for 2007 - 2012 are preliminary and

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

d Estimated abundance of green sturgeon >40 inches in total length, 1992-2012. Estimates for 2006, 2007, 2008, and 2009 are preliminary and

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

e Estimated abundance of 15-year-old white sturgeon, 1992-2012. Estimates for 2006, 2007, 2008, and 2009 are preliminary and subject to

 change.
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

Watershed

Total actions and 

evaluations in Final 

Restoration Plan

Actions and 

evaluations

completed to date

Actions and 

evaluations 

addressed in 

2013

% 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 2 0

Yuba River 14 0 4 0

All Watersheds1 289 67 42 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 1992-2013
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 15

FISHERIES

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 presents the average 

natural production estimate by species since 1992, 

including the most recent data available.

The Central Valley Chinook salmon (all races) natural 

production average from 1992-2012 was 398,585 

fish which dropped below the 1967-1991 baseline 

average Chinook salmon production of 497,054. This 

may be due to the continued lower production returns 

of fall run fish in 2012 that totaled 293,985 fish (Table 

2). Average Chinook salmon natural production for 

the period 1992-2012 has exceeded the watershed 

doubling goal target on Clear Creek, Butte Creek, 

and Battle Creek, and in 2012 the Mokelumne River 

observed high returns (12,484 naturally produced fish) 

(Table 5). Substantial gains in fish populations have 

been observed where investment in flow and passage 

has occurred. Clear Creek and the Mokelumne River 

have also had a substantial investment in habitat 

restoration. The Mokelumne River fish poplulations 

are also aided by non-AFRP organizations, such 

as East Bay Municipal Utilities District, that conduct 

restoration activities. Winter-run natural production 

numbers had continued to trend upward since 1994 

until the poor returns in the last six years (2007-2012). 

Spring-run numbers have trended upwards since 

1991, and production increased in 2012 to 30,522 

naturally produced fish. 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 2012. 

Late fall-run production had increased after 1997, but 

production decreased and has stayed low after 2007. 

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 1992-2012. Available data are 

insufficient 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 midwater trawl index 

for juvenile American shad in the Sacramento-San 

Joaquin River Delta and San Pablo and Suisun bays 

Watershed 53 Structural Actions 75 Non-structural Actions

Number of structural 

actions completed 

in FY 2013*

Number of structural 

actions completed 

since 1992

Number of 

non-structural actions 

completed in 

FY 2013*

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

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 2013, 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) 
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

Watershed Species Doubling Goal Target

1992-2012 Average 

Natural Production 

Numbers Percent of Target

American River* Fall-Run 160,000 104,751 65.5

Antelope Creek Fall-Run 720 0 0

Battle Creek* Fall-Run 10,000 17,610 176.0

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 2,251 150.0

Clear Creek Fall-Run 7,100 10,663 150.0

Cosumnes River Fall-Run 3,300 814 24.7

Cottonwood Creek Fall-Run 5,900 1,950 33.0

Cow Creek Fall-Run 4,600 1,876 40.8

Deer Creek Fall-Run 1,500 865 57.7

Feather River* Fall-Run 170,000 89,922 52.9

Merced River* Fall-Run 18,000 6,517 36.2

Mill Creek Fall-Run 4,200 1,838 43.8

Miscellaneous Creeks Fall-Run 1,100 78 7.1

Mokelumne River* Fall-Run 9,300 8,556 92.0

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

Sacramento River Fall-Run 230,000 70,485 30.6

Stanislaus River Fall-Run 22,000 5,180 23.5

Tuolumne River Fall-Run 38,000 6,634 17.5

Yuba River Fall-Run 66,000 30,983 46.9

Central Valley Wide Fall-Run 750,000 356,780 47.6

Battle Creek* Late-fall-Run 550 677 123.1

Sacramento River Late-fall-Run 68,000 17,367 25.5

Central Valley Wide Late-fall-Run 68,000 17,218 25.3

Butte Creek Spring-Run 2,000 14,525 726.2

Deer Creek Spring-Run 6,500 1,984 30.5

Mill Creek Spring-Run 4,400 1,204 27.4

Sacramento River Spring-Run 59,000 684 1.2

Central Valley Wide Spring-Run 68,000 18,397 27.0

Calaveras River Winter-Run 2,200 0 0

Sacramento River* Winter-Run 110,000 6,191 5.6

Central Valley Wide Winter-Run 110,000 6,191 5.6

TOTAL All races 990,000 398,585 40.3

* Watersheds that contain a fish hatchery.

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

Doubling Goal Targets, 1992-2012
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 17

FISHERIES

suggests the AFRP production target for this species 

was met in three of 21 years between 1992 and 

2012. The 2012 midwater trawl index for this species 

(414) decreased from 2011 (892), and the 2012 

index was markedly below the 1967-1991 baseline 

average of 2,129 shad and the AFRP production 

target of 4,300 shad. Monitoring of legal-size striped 

bass in the Central Valley’s anadromous waters has 

occurred in 16 out of 21 years between 1992 and 

2012 and the AFRP production target has not been 

met. 

About 23% of all Restoration Plan actions and 

evaluations (67/289) have been completed in the 

1992 to 2013 time period (Table 3). Of the 128 

“time certain” high and medium priority actions, 

forty-six (36%) have been completed since 1992 

(Table 4). Although structural or non-structural actions 

were not completed in FY2013, various projects to 

address high priority limiting factors in 20 watersheds 

continued, including fish passage, entrainment, habitat 

restoration, and spawning gravel augmentation 

projects as well as variety of assessments and 

evaluations that are providing information critical for 

future projects.

Accomplishments in the Sacramento 

Basin

American River – A structured decision making 

(SDM) prototype model was developed and further 

refined to assist in selecting the best actions for 

restoration given existing conditions, e.g., spawning 

versus rearing habitat. Additional spawning and 

side channel habitat was restored in FY2013 with 

the addition of 4,000 cubic yards of gravel. An 

additional 2,000 cubic yards of coarse material 

was used to raise the bed elevation in the spawning 

area and stabilize areas of active sediment transport. 

Floodplain benches were also built and instream 

woody material placed in the restored side channel to 

enhance rearing habitat for juvenile Chinook salmon 

and Central Valley steelhead. This project is coimplemented 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 FY2013, the Tehama County 

Resource Conservation District completed additional 

analysis to evaluate various alternatives for juvenile 

fish passage. The Technical Advisory Committee has 

met with the diverters to determine the most feasible 

alternative. A final report of the project’s history, 

along with identifying data gaps discovered during 

detailed design discussions, will be completed early in 

2014. This project was a cooperative effort between 

the USFWS, National Marine Fisheries Service 

(NMFS), CDFW, and the Tehama County Resource 

Conservation District.

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. In FY 2013, the riparian planting portion 

of the project was completed. The December 2012 

storm slightly damaged the road and abutment fill on 

one end of the bridge which was repaired this year. 

Monitoring of the streambed for future adjustment 

occurred in November 2012 prior to the storm and 

was re-surveyed this year. This project improved 

passage to 6.5 miles of spawning and holding habitat. 

This project was a cooperative effort between the 

USFWS and CDFW.

In 2013, additional stream gages were installed 

and water quality monitoring was initiated to collect 

additional information for the Lower Antelope Creek 

Geomorphic Analysis in Tehama County (Evaluation 

1). 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 
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

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). The additional pending work has been 

delayed to be completed until 2016. This project is a 

cooperative effort among the U.S. Department of the 

Interior, USBR, USFWS, NMFS, CDFW, and the Pacific 

Gas and Electric Company (PG&E).

Bear River – AFRP reviewed existing temperature 

data, field notes, and satellite imagery to identify 

appropriate locations to conduct more detailed habitat 

typing and snorkel surveys in Dry Creek (tributary 

to the Bear River) on Beale Air Force Base and in 

the Spenceville Wildlife Area. 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 

(Action 2) were completed in 2012 and the final report 

was completed in 2013. 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 the 

addition of new stream gages and surveys were 

implemented in 2013. The USFWS also identified 

and established index sites and continued to track 

changes in anadromous fish habitat through 2012 and 

2013. The USFWS also completed fish surveys from 

the confluence with the Sacramento River upstream 

for approximately 19.2 miles. The survey extended 

from 9 October 2012 through 27 November 2012 

and encompassed a majority of fall-run Chinook 

salmon spawning in Cottonwood Creek. Coded-wire 

tags, biological and genetic samples, and associated 

information were collected. A final report on the 

sediment budget project is anticipated to be completed 

in 2014.

The Nonnative Invasive Plant Management and 

Control Project (Action 5) continued treatments to 

remove nonnative invasive plants in Cottonwood 

Creek. In early October of 2012, four miles 

(76.75 acres) of cut stump treatment to Salt Cedar 

(Tamarix sp) was applied and the treatment was 

repeated again on September 2013. 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 2013, AFRP staff attended six technical team 

meetings to review draft documents and develop 

the alternatives analysis (Phase 1) for the South Fork 

Cottonwood Creek Fish Passage Improvement Project 

(Central Valley Evaluation 11). A selected alternative 

is being prepared for the final design phase and the 

environmental compliance and permitting steps have 

been initiated. This project is a cooperative effort 

between the USFWS, CDFW, USBR, NMFS, and the 

landowner. 

Cow Creek – The designs were completed and 

permitting initiated in 2013 for the Clover Creek Fish 

Passage/Millville Diversion Dam Restoration Project. 

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, 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. In 

FY 2013, Stillwater Sciences staff reviewed the draft 

vegetation maps prepared by AIS and completed 

the field verification and conditions assessment visits 

during the summer of 2013. Next, the final vegetation 

maps will be prepared and potential restoration sites 

will be identified. 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 man-made barriers and diversions. Field surveys 

were implemented in 2013. This is a cooperative 
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 19

FISHERIES

project with the USFWS, CDFW, Cow Creek 

Watershed Group, and the Western Shasta Resource 

Conservation District.

Deer Creek – Field site surveys were completed 

during the low flow period in the summer of 2013 for 

the Lower Deer Creek Falls Fish Passage Improvement 

Project (Phase 1). This project will 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, NMFS, USBR, CDFW, and 

the Deer Creek Irrigation District.

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. In 2013, fish 

collection sites and techniques were agreed upon 

by the agencies. The initial collection and acoustic 

tagging of wild juvenile Chinook salmon occurred 

in the spring of 2013. Data has been collected and 

is currently being analyzed. An additional year of 

funding has been added to the agreement. 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 

Feather and Yuba rivers in FY2013. DIDSON surveys 

began February 15, 2013 in the lower Feather River. 

As of July 22, 2013, CDWR completed 49 surveys at 

13 sites for a total of about 19 hours of footage. They 

recorded 4 sturgeon images at Beer Can Beach (RM 

8.8) and had 24 detections below Shanghai Bend 

(RM 24.5), which they estimate represent between 

3-5 fish. Three green sturgeon were collected and 

acoustically tagged. The DIDSON also helped 

determine where to deploy egg mats in an effort to 

document spawning. No green sturgeon eggs were 

collected. This is a cooperative project between 

the USFWS and CDWR whom cost shared about 

$20,000 in in-kind services. 

Mill Creek – The Mill Creek fish passage assessment 

and restoration project was funded in FY2011 and 

additional funding to complete the environmental 

permitting was modified into the agreement on 

September 2013 (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 the alternatives report 

was finalized in 2013. Final designs for the three 

sites should be completed in early FY 2014. 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. In FY 2013, 

Stillwater Sciences staff reviewed the draft vegetation 

maps prepared by AIS and completed the field 

verification and conditions assessment visits during 

the summer of 2013. Next, the final vegetation maps 

will be prepared and potential restoration sites will 

be identified. This is a cooperative project with the 

USFWS, CDFW, and the Mill Creek Conservancy. 

Sacramento River – Redd stranding surveys were 

implemented between January 11, 2013 and March 

19, 2013 in the upper mainstem Sacramento River. 

Eighty-one redds were observed and monitored 

of which twelve redds were documented as being 

dewatered during the sampling period. In the spring 

of 2013, fish stranding surveys were implemented 

to observe and report on locations (side channels, 

pools) that could potentially contain stranded juvenile 

salmonids that were isolated to varying degrees 

by flow reductions. During the survey season, 

seventy-two separate stranding locations between 

the Keswick Dam (the uppermost limit of anadromy 

on the mainstem Sacramento River) and the Red 

Bluff Diversion Dam (a total of fifty-nine river miles) 

were observed. An Annual Report was completed 

summarizing the 2012/2013 redd dewatering and 

juvenile fish stranding data. 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 
20 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

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 – Four acres were planted with 4,700 

cottonwood and willow pole cuttings to restore 

riparian habitat on Hammon Bar in FY2013, raising 

the total area planted for the project to five acres. 

Overall first year survival was 80% for FY2012 

plantings, but fell to 50% for FY2013 plantings due to 

the very dry conditions. The planting area is intended 

to flood periodically under moderate flows and thus 

provide juvenile salmonids with improved rearing 

habitat (Evaluation 4). This project is a cooperative 

effort between the USFWS, CDFW, Bureau of 

Land Management (BLM), Americorps, Western 

Aggregates, PG&E, and the South Yuba River Citizens 

League. PG&E is cost sharing $50,000 of the total 

project cost.

The Yuba River Study Utilizing the Spawning Habitat 

Integrated Rehabilitation Approach (SHIRA) has led 

to a detailed map and 2-D model of the lower Yuba 

River. Mapping of the final reach (i.e., the Narrows) 

was completed as part of a related AFRP project. 

Reports assessing the 2012 data were presented at 

the Lower Yuba River Accord Symposium on June 12th, 

2013. AFRP staff continued to be an active participant 

on the Yuba Accord RMT providing technical expertise 

on anadromous fish habitat restoration and guiding 

future restoration efforts with the SHIRA model. This 

project is a collaborative effort between the USFWS, 

NMFS, Army Corps of Engineers (ACOE), Yuba 

County Water Agency (YCWA), and the University of 

California at Davis. ACOE provided $100,000 and 

YCWA contributed $30,000 in cost-share to further 

refine the model. 

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 2012 data were presented at 

the Lower Yuba River Accord Symposium on June 12th, 

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, YCWA, 

and the Pacific States Marine Fisheries Commission. 

YCWA provided $120,000 for in-kind services to 

operate and maintain the fish counting systems on both 

ladders at Daguerre Point Dam. 

Accomplishments in the San Joaquin 

Basin

Calaveras River – The Caprini Low Flow Crossing 

Fish Passage Project was completed this fiscal year 

on September 2013. This project restored access to 

about 6 miles of habitat (Action 3). Final designs were 

completed and permitting initiated for the California 

Central Traction Railroad bridge site. Both projects 

are a cooperative effort between the USFWS, 

CDFW, CDWR, Stockton East Water District, Fisheries 

Foundation of California, and the University of the 

Pacific. Stockton East Water District is cost-sharing 

$200,000 of the total project cost. 

Cosumnes River – Post-project monitoring for the 

Cosumnes River Passage Improvement Project was 

continued in 2013. A DVR security camera system, 

trail cameras, and a VAKI Riverwatcher fish counting 

system were installed at North Granlees Dam 

Fish Ladder and Rooney Dam (a downstream site 

remediated in 2010). Using the data gathered by 

these devices, an escapement estimate of 1,071 fallrun Chinook salmon was developed. The monitoring 

also confirmed that the rebuild of the North Granlees 

Fish Ladder is performing as designed and fish are 

easily passing at a wide range of flows and conditions. 

This project improved fish passage at Rooney Dam 

and North Granlees Dam restoring unimpeded access 

to anadromous fish in the Cosumnes River (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). The NEPA, 

National Historic Preservation Act Section 106, ESA, 

Clean Water Act Section 404 and 401, and other 

applicable permits were developed. Pre-project 

biological and physical survey activities funded in 

2012 were completed. This project is a cooperative 

effort between the USFWS, CDWR, Ducks Unlimited, 
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 21

FISHERIES

ACOE, and BLM. Ducks Unlimited and the ACOE cost 

shared an estimated $800,000.

Merced River – AFRP staff continued to administer the 

rotary screw trap monitoring agreement with Merced 

Irrigation District. This project documented the number 

of juvenile salmon and steelhead that outmigrated 

from the Merced River in 2013. Estimates of juvenile 

salmonid production were calculated and the existing 

outmigration database was updated. Additional 

data to assess effectiveness of flow management and 

habitat restoration projects was collected. Merced 

Irrigation District cost shared about $300,000 for 

the operation of the rotary screw traps from January 

5th to June 15th, 2013 and a fish counting weir from 

September 29th to December 31st, 2012.

Designs and permitting for the Merced River floodplain 

and channel restoration project at Snelling (Action 3) 

were completed in 2013. The objective of the project 

is to improve spawning and rearing habitat for juvenile 

salmonids on the Merced River by restoring areas 

degraded by gold mining operations. Pre-project 

monitoring which included 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. Approximately 

48,136 yds3 of gravel was excavated from the 

floodplain in December 2012. During July–August 

2013 18,196 yds3 of spawning gravel material and 

7,965 yds3 of cobble material were generated from 

dredger tailing material remaining in the floodplain 

feature area. A stockpile of 3,164 yd3 of spawning 

gravel was left on-site for placement in river next 

year. In total, 22,997 yds3 of screened material were 

placed in the Merced River from 29 August to 25 

September 2013. This project is a cooperative effort 

between the USFWS, CDFW, and Merced County.

The final year of construction activities on the Merced 

River Ranch Project was completed on September 

2013 where approximately 87,222 cubic yards of 

material were excavated and sorted to restore the 

floodplain and channel. An estimated 26,848 cubic 

yards of gravel was placed in the Merced River to 

enhance spawning habitat. The Merced River Ranch 

Floodplain Enhancement Project restored 4.28 acres 

of riparian floodplain, created a 0.27 mile long 

side-channel, and restored 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 FY2013. Staff 

reviewed and provided comments on the Updated 

Study Report and various Technical Memorandums on 

channel armoring, IFIM habitat modeling, temperature 

criteria, 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 – Ongoing habitat assessments 

and modeling of the treatment reaches and 

downstream affected areas has been completed 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 was completed in 2013. This project is a 

cooperative effort between the USFWS and the East 

Bay Municipal Utility District (EBMUD). 

In FY2013, 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 (about 5,000 

acre feet) with Delta Cross Channel (DCC) operations 

in an effort to improve adult Chinook salmon returns 

(Delta Evaluation 5). The DCC gates were not closed 

in October of 2012 due to low flow conditions and 

water quality concerns in the South Delta. About 

80 adult Chinook salmon were acoustically tagged 

before, during, and shortly after the Mokelumne River 

fall pulse flow. Preliminary results of this experiment 

found that straying of Mokelumne River origin fish 

can be reduced considerably with fall pulse flows 

and closing the DCC during a portion of October. 

Modifications to DCC operations can be used to help 

AFRP achieve its doubling goal in the Mokelumne 

River. This project is a cooperative effort between 
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

the USFWS, NMFS, CDFW, Woodbridge Irrigation 

District, and the EBMUD. 

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 and underwater video survey 

techniques to identify and map 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 and 19 white sturgeon were captured 

and implanted with acoustic transmitters in 2012 and 

2013, respectively. 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 habitatrelated physical characteristics along the San Joaquin 

River with a multibeam sonar, acoustic Doppler current 

profiler, and RTK-GPS. 

Stanislaus River – FY 2013 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 report summarizing the FY12 salmonid 

production data was completed. The second year 

of the Chinook salmon juvenile acoustic study was 

completed this year and the annual report was 

submitted. Juvenile salmon were radio tagged and 

tracked using both fixed and mobile detectors. The 

study will identify geographic sources of mortality for 

juvenile salmonids within the migratory corridor and 

evaluate the effectiveness of improving survival with a 

spring pulse flow. These studies assist with evaluating 

benefits resulting from habitat restoration actions. TriDam cost shared about $300,000 for the operation 

of the rotary screw traps from January 1st to June 15th, 

2013 and the fish counting weir from September 11, 

2012 to June 30, 2013.

A construction summary report of the Lancaster Road 

Floodplain and Side-channel Restoration Project 

was completed in 2013. Additional post-project 

monitoring was undertaken and results were presented 

at professional conferences. Post-project monitoring 

which included vegetation surveys, 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 

Honolulu Bar Floodplain Restoration Project. 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, River 

Partners, and CDFW. 

Planning documents and design alternatives 

were developed for the Knights Ferry Floodplain 

Restoration Project and the Buttonbush Floodplain 

Restoration Project (Action 2). Pre-project monitoring 

data was collected to characterize the pre-project 

habitat conditions including water depth and 

velocities, substrate size distribution, and biological 

data. Topographic and bathymetric surveys were 

also completed to be used to further refine design 

alternatives. These projects are a cooperative effort 

between the USFWS and the ACOE. 

The Fourth Annual Stanislaus River Salmon Festival 

was held on November 3rd, 2012 at the Knights Ferry 

Recreation Area, with AFRP staff heavily involved in 

the 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 sampled 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 in 2011. 

Adult and juvenile salmon were observed using the 

improved habitat October 2012 - May 2013. The 

Final Report was completed in 2013. This project 

was a collaborative effort between USFWS, CDFW 

Ecosystem Restoration Program, and Friends of the 

Tuolumne River.
ANADROMOUS FISH RESTORATION PROGRAM 3406 (b)(1) 23

FISHERIES

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 FY2013 and submitted study proposals 

for Floodplain Habitat Modeling, juvenile Chinook 

salmon and predator acoustic telemetry studies, and 

a predator mark and recapture study. Staff also 

provided detailed comments on the Don Pedro FERC 

Initial Study Report and on the Don Pedro Chinook 

Population Model. 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.

Aerial photograph of habitat restoration work at the Merced River Ranch that was completed in 2013. Work included the 

introduction of over 91,000 cubic yards of spawning gravel and construction of a 1,426 foot side channel and 4.28 acre floodplain. 

This project addresses multiple limiting factors for salmonids in the Merced River, including limited quality and quantity of 

spawning habitat for adults, limited rearing habitat for juveniles, and degraded riparian habitat and river function.
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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 2013 ACCOMPLISHMENTS

The BDO obligated $6,247,000 from the Bay-Delta 

Fund in FY13. 

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 third 

year of 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 is in review. 

The BDO also continued funding for: (1) development 

of a life cycle model for delta smelt; (2) 3-dimensional 

hydrodynamic/particle tracking modeling in support of 

studies of delta smelt hatching distribution simulations 

and and juvenile salmon migration studies; (3) the 

six-year study of juvenile steelhead survival in the south 

Delta (required under the NMFS Biological Opinion); 

(4) a NMFS study of the genetic impacts of hatcheries 

on wild stocks; (5) a NMFS study on how large intake 

structures affect predators and predation on juvenile 

salmonids; (6) 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 (7) 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)

Geospatial data representing that a combination of light, sound 

and bubbles deters juvenile Chinook salmon movement into 

Georgiana Slough to improve survival.
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “Other” & (b)(23) 25

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 in 

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 and 

riparian rehabilitation and floodplain infrastructure 

improvements. Together, these actions will increase 

and enhance 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 miles 

of the Trinity River between Lewiston Dam and 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) of coarse 

sediment annually. 

Fine sediment delivery and storage – The program 

aims to reduce fine sediment delivery from tributary 

watersheds by 10,000 to 20,000 CY annually. 

Additionally, the goal for fine sediment management 

is to transport as much or more fine sediment 

downstream as is delivered to the upper river from 

tributary watersheds to reduce in-channel storage.

Channel rehabilitation – The goal of the channel 

rehabilitation component of the program is to restore 

functioning alluvial river attributes and increase 

salmonid freshwater habitat. The ROD calls for 44 

bank rehabilitation projects and 3 side channels, 

which combine to make 47 sites. Channel restoration 

progress is currently measured by the number of 

Trinity River Restoration 

Program

 3406 (b)(1) “Other” & (b)(23)
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

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 2013 ACCOMPLISHMENTS 

In FY 2013, the Trinity River Restoration Program 

obligated $3,214,440 from the Water & Related 

Resources Fund (b)(23), $10,782,901 from the Water 

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

Funds of $1,997,143. 

Flows – Water Year 2013 was a Dry Water Year. 

Water temperature, channel rehabilitation construction, 

juvenile salmonid numbers and available habitat and 

riparian vegetation issues were considered in flow 

scheduling. The ROD prescribed flow for a dry water 

year is 453,000 AF. 

Water volume peak flow was modified from 5 days to 

a 2 day peak at 4,500 cfs to facilitate an extended 

springtime flow of 8 days at 2500 cfs to provide 

additional rearing habitat for a large year class of 

juvenile salmon. 

Course Gravel and Channel Rehabilitation – The 

Trinity Management Council approved 200 CY of 

gravel be injected at the Lewiston Diversion Pool 

during the 4,500 cfs peak flow, and another 1500 

CY for dry placement at the Sawmill rehabilitation site. 

Channel rehabilitation projects were implemented at 

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 1,890 19,175 8,918 12,347 11,566

 

1

 2013 data is not available until January 2014.

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 winter

 run 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
TRINITY RIVER RESTORATION PROGRAM 3406 (b)(1) “Other” & (b)(23) 27

FISHERIES

Table 7: Annual ROD Flows and Peak Releases to Trinity River, 2006-2013

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

2013 Dry 453,000 AF 453,000 AF 4,500

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

Lorenz Gulch and Douglas City encompassing 2 more 

sites contributing to the 47 sites included in the ROD 

for a total of 32 sites completed. The program also 

continued planning and engineering designs for the 

next four channel rehabilitation projects. 

Five watershed projects including watershed condition 

assessments and educational outreach activities 

were completed in FY 2013 that kept approximately 

15,500 CY of fine sediment out of the mainstem.

Monitoring and Assessment – Approximately 

$5 million was obligated in FY 2013 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 

are shown in Table 6. 2013 data was not available as 

of the date when this report was developed.

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/).

Strategic placement of large boulders in the Trinity River mainstem and constructed split flow channels creates additional fish 

holding habitat for adult salmon and steelhead.
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

Table 9: Rehabilitation Site Construction Summary, 2005-2013 

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

2013 Lorenz Gulch 2 56,400 525 1.4 52

Total 30 763,350 2,185 15.30 304

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

Table 8: Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2013

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

2013 High Flow Injections 200 1,700

Saw Mill Dry Placement 1,500

Total 48,700

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

permanent in-river features.
TRACY (JONES) PUMPING PLANT PROGRAM 3406 (b)(4) 29

FISHERIES

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

capable of pumping between 800 - 1000 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 2013 ACCOMPLISHMENTS 

The program obligated $1,354,568 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 moved from design engineering and 

biological assessments into contracting in support 

of Action 17 which will improve the louver cleaner 

systems and allow the louvers to screen fish more 

efficiently. The contract for the Secondary Louver 

Replacement project was awarded September 6, 

2013. Installation will take place in spring 2014, in 

effect becoming a prototype for Action 18. Also, 

work continued 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. The project 

was funded with RAX Program funding. 

The program continued assessments, search of land 

records and initial reconnaissance was 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 

salmon, and evaluation of predatory impacts within 

the secondary system of the TFCF, and investigated 

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 

Tracy (Jones) Pumping Plant

Program

 3406 (b)(4)
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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

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 Fish Facility Improvement Program Publication 

for FY2013:

Tech. Bul. 2012-1

Reyes, R., Z. Sutphin, and B. Bridges. 2012. Effectiveness 

of Fine Mesh Screening a Holding Tank in Retaining 

Larval and Juvenile Fish at the Tracy Fish Collection 

Facility. Tracy Fish Collection Facility Studies. Tracy 

Technical Bulletin 2012-1. U.S. Bureau of Reclamation, 

Mid-Pacific Region and Denver Technical Service Center. 

20 pp.

Volume 48

Svoboda, Connie and M. Horn. 2013. Laboratory Design 

and Testing of an Electrical Crowder for Predator 

Reduction at the Tracy Fish Collection Facility. Volume 

48. U.S. Bureau of Reclamation, Mid-Pacific Region and 

Denver Technical Service Center. 45 pp.
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 31

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 spring 

run Chinook on Clear Creek, restoration actions will 

also help increase spring-run Chinook populations, 

contributing to the CVPIA’s Central Valley-wide goals.

Fish Passage – The fish passage target was achieved 

in 2000, when McCormick-Saeltzer Dam was 

removed, opening 12 additional miles of habitat to fish 

passage and upstream spawning.

Erosion Control – The erosion control target was 

achieved ahead of schedule. All feasible and cost 

effective 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 of July 2012. The federal 

and state lands affected by the Dale Fire have been 

subject to some post-fire stabilization measures such as 

grass-seeding, straw mulching, replanting, and other 

erosion reduction efforts. The Clover Fire of September 

2013 affected the Cottonwood Creek drainage and 

also burned a smaller area within the Clear Creek 

watershed. The potential impacts to Clear Creek are 

not yet fully known.

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, 

Clear Creek Restoration 

Program

 3406 (b)(12)
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPORT

FISHERIES

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

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

two consecutive days of releases when exceeding the 

temperature target. The timing of flows benefit both 

spring run and fall run Chinook but are especially 

important to spawning spring run Chinook as they 

can only spawn in water cold enough to sustain eggs 

through their incubation period. 

Since 1999, studies have been undertaken by CVPIA 

and CALFED to develop channel maintenance 

flows, which are vital for providing and maintaining 

spawning and rearing habitat in Clear Creek. In 

2008 FWS and CALFED contracted to facilitate a 

pilot re-operation of Whiskeytown reservoir to achieve 

the channel maintenance flow prescription. This 

Environmental Water Program prescription calls for the 

re-operation of Whiskeytown Dam, between March 

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

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

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

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

duration could reactivate 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 2013 ACCOMPLISHMENTS

In FY 2013, the CCRP obligated $612,992 from the 

Restoration Fund and no funding from the Water and 

Related Resources fund.

Gravel Placement (Creation of Spawning 

Habitat) – Spawning gravel was not placed in Clear 

Creek during FY 2013 due to limited funding, but will 

resume in FY 2014.

The second annual evaluation of spawning gravel 

implementation and monitoring was previously 

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 conducts on-going 

monitoring of the spawning gravel and documents 

the areas being used by salmonids for spawning. 

These efforts will evaluate the efficacy of the new 

criteria, and identify whether the criteria needs to 

be adaptively changed. The monitoring efforts also 

provides a scientifically-based basis for determining 

future injection locations and amounts.

Channel Restoration – Phase 3C, the last phase 

of the restoration project, will be considered for 

implementation in future years. FWS and BOR began 

initial efforts to garner funding support from the CVPIA 

program managers, and the approval of the Clear 

Creek Technical Team (CCTT) to begin planning efforts 

for this final phase. The FWS and BOR will start by 

working on the feasibility design aspects of the project. 

Thereafter, FWS and BOR will develop a Performance 

Work Statement to begin the process of securing a 

contractor to work on the NEPA/CEQA environmental 

compliance requirements.

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, the numbers 

of spring-run Chinook increased from 8 in 2011 to 68 

in 2012, and 652 were observed in 2013, the highest 

since monitoring efforts began in 1998. 

The pulse flows conducted in Clear Creek are 

beneficial in attracting fish and promoting upstream 

movement. In the spring of 2013, 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 undergoing 

finalization. The strong return of Spring Chinook in 

2013 and their response, particularly to the second 

pulse event (400 pre-pulse, 561 post-pulse; 40% 

increase) provided an objective means to demonstrate 

the importance of pulse flow events in benefitting 

upstream movement. Similar flows will occur each 

year as directed by the NMFS OCAP BO. 

Water temperature targets were met 99% of the time 

due to the large amount of water brought over from 

the Trinity River through Whiskeytown Reservoir. The 

60°F target from June 1 through September 14 was 

achieved 100% of the time and the 56°F target from 

September 15 to October 31 was met 96% of the time.
CLEAR CREEK RESTORATION PROGRAM 3406 (b)(12) 33

FISHERIES

In 2012, the juvenile salmonid flow habitat 

relationships Instream Flow Incremental Methodology 

(IFIM) draft report was released for peer review. 

Work continued on bio-validation of the models. 

The resulting 14 IFIM flow-habitat models is being 

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, and upon its completion, the CCTT 

will provide the report and its recommendations 

to Reclamation. Reclamation will then submit their 

recommendations to NMFS for review and approval.

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. During FY 2013, draft 

technical documents were provided to the CCRP for 

initial review. FWS, Reclamation, and CDFW will 

need to complete formal reviews of these documents 

to enable their finalization. Thereafter, it is expected 

that Reclamation will begin formal development of the 

NEPA/CEQA process.

Adaptive Management and Monitoring

Spawning gravel-size specifications improved 

based on monitoring – Past 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. Gravelsize 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 Graham Matthews and 

Associates (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. As gravel placement did not take 

place in 2013, future project efforts will be monitored 

to evaluate the efficacy of the size criteria which was 

developed in concert with the CCTT.

Phase 3b restoration, pedestrian bridge, 

and Lower Clear Creek Aquatic Habitat and 

Mercury Abatement Project (formerly longterm gravel supply project) – In 2013, planning 

activities continued to obtain permits to conduct 

decommissioning of roads used during habitat 

restoration activities within the Phase 3B areas, 

and planting riparian and upland areas. The future 

decommissioning of roads will reduce the amount of 

habitat fragmentation. Also, the Horsetown pedestrian 

bridge was completed. The long-term gravel supply 

project planning and environmental compliance 

activities for this project continued in 2013. The final 

EA/EIS is nearing completion, and is expected to be 

released to the public in early 2014. In addition, the 

final proposal for this 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. Funding from the Ecosystem 

Restoration Program will allow completion of project 

construction. 

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. These actions 

indicated that the fine material has been progressively 

moving downstream and out of the Clear Creek 

system. It appears possible that the amount of fine 

sediment has been decreased, perhaps by the multiple 

pulse flows that have occurred since the fire. Since 

the 2008 fires, the juvenile productivity of steelhead 
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2012 ANNUAL REPORT

FISHERIES

and spring and fall Chinook had decreased, although 

it is was not understood why. Recent monitoring by 

the FWS has indicated that productivity of juvenile 

salmonids may be increasing. Since the recent 2012 

Dale Fire, and the Clover Fire of 2013, monitoring 

efforts need to continue in Clear Creek system to guide 

future restoration actions. 

Fish and geomorphic monitoring results may 

improve future pulse flows – Results of past and 

recent pulse flows 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 CCTT has assisted in adaptively modifying 

pulse flows in an effort to move more sediment 

downstream, as well as attracting Spring-run Chinook 

and stimulating their upstream movement. Therefore 

in 2013 both higher and lower pulse 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 constraints, and adaptive management. 

This proposal was prompted by the results from ongoing 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. The 2012 fallrun estimate was 7,631. The 2013 escapement is not 

yet available. 

In addition, populations of threatened spring-run 

Chinook and steelhead have been re-established 

in the Clear Creek watershed. The recent CDFW 

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 CDFW to build and install a 

fish counting weir in Clear Creek near the confluence 

with the Sacramento River. The weir was in operation 

during 2013 by CDFW, using video and DIDSON 

sonar technology for fish counts.

EDM Total Station (digital survey apparatus) was used to map 

streambed elevations in Clear Creek.

Geomorphologists performing bedload sampling at the Clear 

Creek Igo site using a cataraft vessel.
SPAWNING AND REARING HABITAT RESTORATION PROGRAM 3406 (b)(13) 35

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 California Department 

of Fish and Wildlife (CDFW) in the Sacramento, 

American and Stanislaus rivers; juvenile production 

monitoring conducted by FWS in the Sacramento 

River (Reclamation funded), FWS and the Pacific 

States Marine Fisheries Commission in the American 

River (CVPIA funded), and private contractor in the 

Stanislaus River (CVPIA funded). 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 (see Table 11). 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 2013 ACCOMPLISHMENTS 

In FY 2013, the SRHP obligated $620,753 from the 

Restoration Fund.

Spawning and Rearing Habitat 

Restoration Program

 3406 (b)(13)
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

Sacramento River – In 2013, the program placed 

14,000 tons of gravel just below Keswick Dam, or 

140% of the annual target of 10,000 tons. This gravel 

is distributed downstream with high flows. Redd 

surveys funded separately by Reclamation showed 

that 75% of the winter-run Chinook salmon spawning 

occurred upstream of the Anderson Cottonwood 

Irrigation District diversion dam in 2013. 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 2013, no projects were 

implemented by the program in the Stanislaus River. 

Monitoring conducted by the program consisted of 

redd surveys and surveys of downstream movement 

of previously placed gravel During redd surveys in 

November and December of 2012, 285 Chinook 

salmon redds were mapped on the gravel placed in 

Goodwin Canyon at the float tube pool and cable 

crossing sites. The peak river-wide redd count was 

1,023 redds. The redds on the Goodwin Canyon 

sites made up 28% of the peak river-wide count. In 

addition, high densities of rearing juvenile rainbow 

trout/steelhead, a threatened species in the Stanislaus, 

were documented rearing at the Goodwin gravel 

placement sites during snorkel surveys throughout 

the year. The primary source of gravel to Goodwin 

Canyon since Goodwin Dam was built has been 

the recent gravel placements (over the last 15 years 

or so) so the cumulative movement of this material 

can be visually monitored with snorkel surveys in the 

canyon. A 2013 survey showed gravel accumulations 

creating spawning habitat 0.2 mile downstream of 

the placement reach. No gravel has reached the 

downstream end of the large pool at the old stream 

gauge site located 0.5 mile downstream of the gravel 

placement site and one mile downstream of Goodwin 

Dam.

American River – In 2013, the SRHP placed 6,000 

tons of gravel and improved a 400-yard long side 

channel at River Bend Park. The gravel placement 

represented 86% of the annual target of 7,000 tons. 

This project was funded by SRHP and AFRP and 

included participation by multiple agencies including 

Reclamation, Fish and Wildlife Service, the Water 

Forum, City of Sacramento, CDFW, and Sacramento 

County Regional Parks. The project included a 

designed channel spanning gravel placement 

(creating approximately 5500 square yards of 

improved spawning habitat) and enhanced a side 

channel to reduce stranding of juvenile salmonids at 

low flows and improve juvenile rearing habitat by 

incorporating woody material and widening the side 

channel. 

The program continued development of a decisionsupport model using the Structured Decision Making 

approach to help determine the most efficient use of 

management resources to maximize the number and 

condition of juvenile salmonids leaving the American 

River. We improved on the predictive model created 

in FY12 by 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 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. In addition to reports 

submitted to the (b)(13( program, monitoring activities 

resulted in publication of a peer-reviewed paper: 

Zeug, S. C., Sellheim, K., Watry, C., Rook, B., Hannon, 

J., Zimmerman, J., Cox, D. and Merz, J. (2013), 

GRAVEL AUGMENTATION INCREASES SPAWNING 

UTILIZATION BY ANADROMOUS SALMONIDS: A 

CASE STUDY FROM CALIFORNIA, USA. River Res. 

Applic.. doi: 10.1002/rra.2680.
SPAWNING AND REARING HABITAT RESTORATION PROGRAM 3406 (b)(13) 37

FISHERIES

Sacramento River 

(10,000 Ton 

Target)

%

Target

Stanislaus 

River

(3,000 Ton 

Target)

%

Target

American River

(7,000 Ton 

Target)

%

Target

1997 31,000 310 2,000 67 0

1998 23,000 230 3,000 100 0

1999 25,000 250 0 6,000 86

2000 32,000 320 1,300 43 0

2001 0 500 17 0

2002 15,000 150 4,000 133 0

2003 8,800 88 0 0

2004 8,500 85 1,200 40 0

2005 7,200 72 2,500 83 0

2006 6,000 60 2,500 83 0

2007 6,000 60 4,100 137 0

2008 8,300 83 0 7,000 100

2009 9,900 99 0 10,600 151

2010 5,500 55 0 16,000 229

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

2012 15,00 150 3,000 100 24,510 350

2013 14,000 140 0 6,000 86

TOTAL 220,000 130 29,100 57 90,880 76

Table 11: Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2013

Chinook salmon spawning in a gravel enhancement site in the Stanislaus River with excited juvenile steelhead/rainbow nearby.
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

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 

to all interested parties), provide training in data 

management, ensure compliance with relevant federal 

laws and regulations, and ensure the effective and 

economical management of resources.

PERFORMANCE MEASURES

The CAMP has one performance measure. That 

measure requires that the program produce one report 

each year.

The CAMP Implementation Plan identifies 82 

monitoring elements that are required to assess 

progress toward the AFRP fish production targets 

(CAMP Objective #1). The Plan also provides a 

framework to assess the biological response to, and 

effectiveness of, restoration actions (CAMP Objective 

#2). The program’s goals have recently been 

expanded to consolidate, standardize, and enhance 

the collection of data related to the CVP ecosystems 

(CAMP Objective #3).

FY 2013 ACCOMPLISHMENTS 

In FY 2013, the CAMP received $1,386,732 from the 

Restoration Fund.

The CAMP accomplishments that were completed 

in FY 2013 are listed below; the accomplishments 

have been grouped according to the three CAMP 

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 AFRP’s fish production 

targets. 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 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 CAMP depends on other programs and 

agencies that provide information that the CAMP 

then synthesizes and summarizes in its annual report. 

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. That document describes methods for 

monitoring nine anadromous fish taxa in California’s 

Central Valley, and provides procedures for 

assessing the biological results and effectiveness of 

different categories of restoration activities. The nine 

anadromous fish taxa in the Plan are: 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.

Comprehensive Assessment 

and Monitoring Program

 3406 (b)(16)
COMPREHENSIVE ASSESSMENT AND MONITORING PROGRAM 3406 (b)(16) 39

FISHERIES

objectives. For the CAMP-funded project activities 

referenced below where a report was completed, the 

reports can be accessed on the CAMP website at: 

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

CAMP Objective #1

CAMP Annual Report – CAMP produced its 2012 

annual report assessing the overall effectiveness 

of actions implemented pursuant to CVPIA section 

3406(b) in meeting AFRP fish production targets.

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 2013. A 

final report describing this activity was produced. The 

data from the marking and tagging program is used to 

quantify the origin of adult salmon (hatchery vs. wild) 

observed during escapement surveys, and therefore 

yields more accurate natural production estimates for 

Chinook salmon.

Quantify the Proportion of Hatchery vs. WildOrigin Adult Salmon - Cottonwood Creek – A 

report quantifying the relative contribution of hatcheryvs. wild-origin adult salmon in Cottonwood Creek in 

2012 was completed. These data are used to produce 

more accurate natural production estimates for fall-run 

Chinook salmon in the Cottonwood Creek watershed.

Quantify Escapement of Adult Steelhead and 

Spring-run Chinook salmon - Battle Creek – A 

report documenting the escapement levels of adult 

steelhead and spring-run Chinook salmon in Battle 

Creek at the Coleman National Fish Hatchery weir in 

2012 was produced.

CAMP Objective #2

CAMP Rotary Screw Trap Platform – Work 

continued on the development of the CAMP rotary 

screw trap platform. That product has a database 

and programming code that will store/process rotary 

screw trap (RST) data, and be used to develop juvenile 

Chinook salmon production estimates for different 

Central Valley watersheds. A final database structure 

for storing RST data has been created, a user interface 

with various forms for entering new RST data into the 

database is finished, the migration of historical data 

from four watersheds to the database is complete, 

and the development of computer programming code 

that will produce juvenile salmon production estimates 

based on the raw data in the database is nearly 

complete.

Monitor Juvenile Chinook Salmon Production 

- Stanislaus River (Caswell State Park) – Rotary 

screw traps were operated at Caswell State Park on 

the Stanislaus River during the 2013 rotary screw trap 

field season; a report documenting those operations 

will be completed in the fall of 2013. A report 

documenting the results from the 2012 rotary screw 

trap field season at Caswell State Park was completed.

Monitor Juvenile Chinook Salmon Production - 

American River – Rotary screw traps were operated 

on the American River during all of the 2013 rotary 

screw trap field season.

Monitor Juvenile Chinook Salmon Production - 

Clear Creek – A report documenting the production 

of juvenile Chinook salmon and steelhead on Clear 

Creek during the 2012 rotary screw trap field season 

was completed.

Monitor Juvenile Chinook Salmon Production - 

Sacramento River (Red Bluff Diversion Dam) – 

A draft document summarizing rotary screw trap 

operations on the Sacramento River at the Red Bluff 

Diversion Dam during the 2012 rotary screw trap field 

season is being developed.

CAMP 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.
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

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.

Develop a Science Based Management 

Framework – Staff from the U.S. Geological Survey 

were hired and several meetings were held to assist 

with the development of tools and a framework that 

will be used to: (1) revisit CVPIA Program objectives 

and performance measures with State and Federal 

agencies as well as other stakeholders. Reframe 

the objectives and performance measures where 

appropriate, with explicitly stated hypotheses with 

measurable criteria; (2) update/develop a systemwide conceptual/quantitative model for an area that 

includes the Bay-Delta and Central Valley headwater 

tributaries to help guide Program decisions; (3) 

reassess monitoring and evaluation efforts within 

the context of revised objectives and a system-wide 

model; and (4) incorporate scientific reviews into the 

organizational structure of the Program to evaluate the 

Program’s progress.

USFWS Fisheries Technician Duane Linander releasing a White Sturgeon implanted with an acoustic transmitter. Under the 

direction of AFRP biologist Zac Jackson, tracking of adult White Sturgeon will continue for the ten year life of the transmitter. Data 

from this project is critical for resource agencies to protect and manage sturgeon habitat.
ANADROMOUS FISH SCREEN PROGRAM 3406 (b)(21) 41

FISHERIES

The Anadromous Fish Screen Program (AFSP) works 

together with the State of California to construct, 

replace and rehabilitate fish screens 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 can provide matching cost share 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 often complex and are 

sometimes 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 have conducted 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 2013 ACCOMPLISHMENTS 

The AFSP obligated funding from the Restoration Fund 

in the amount of $5,169,957 and $2,800,000 from 

Bay-Delta funds. 

Screening Diversions

Construction was completed on the 389 cfs Natomas 

Mutual Sankey Fish Screen on the Sacramento River 

that replaced two existing diversions on the Natomas 

Cross Canal. This project also resulted in the removal 

of an anadromous fish migration barrier (seasonal 

diversion dam) on the Natomas Cross Canal. 

The AFSP also completed construction of four fish 

screens on the Sacramento River at River Garden 

Farms #3 -Townsite (62 cfs), Alamo Farms #1 (36 cfs), 

Tisdale Irrigation District #2 (44 cfs), Cranmore Farms 

#2 (40 cfs), and one fish screen in the SacramentoSan Joaquin Delta at Joe Sanchez Farms (24 cfs), 

involving installation of state-of-the-art retractable 

cylindrical fish screens. Fish entrainment monitoring 

was also conducted in 2011 and/or 2012 at these 

five diversion locations. This contributed to an effort 

to assess the biological benefits of fish screening on 

the Sacramento River and to help prioritize future 

fish screening efforts. A final report documenting the 

results of this monitoring effort (“Evaluation of Fish 

Entrainment in 12 Unscreened Sacramento River 

Diversions”) was issued in July 2013. 

Anadromous Fish Screen 

Program

 3406 (b)(21)
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

Construction continued on the Yuba City Fish Screen 

consisting of a 74 cfs diversion on the Feather River. 

This project will be completed in FY 2014. 

The AFSP continued to support design, environmental 

compliance, and permitting activities for the following 

fish screen projects: RD 2035/Woodland Davis 

Clean Water Agency Joint Intake (400 cfs), Lake 

Pritchard (150 cfs), and Colusa Indian Community 

Council (22 cfs) on the Sacramento River; : Feather 

Water District North (78 cfs) and South (40 cfs) 

diversions on the Feather River; South Sutter #1 (80 

cfs) on Auburn Ravine , and West Stanislaus Irrigation 

District (347 cfs) on the lower San Joaquin River. 

See Table 12 for fish screen projects constructed by 

watershed using AFSP cost share funding.

Table 12: AFSP Projects by Watershed 

and Cubic Feet per Second (cfs) 

Screened, 1994-2013

Watershed

Number of

 Fish Screens

Flow

(cfs)

Sacramento 26 4,779

American 1 310

Yuba 1 65

Butte 4 257

Delta 7 137

San Joaquin 2 455

TOTAL 41 6,003

Completed River Garden Farms #3 (Townsite) Fish Screen.
SAN JOAQUIN RIVER RESTORATION PROGRAM PUBLIC LAW 111-11 43

FISHERIES

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 CVPIA 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 main stem of the 

San Joaquin River below Friant Dam to the confluence 

of the Merced River, including naturally reproducing 

and self-sustaining populations of salmon and other 

fish.

FY 2013 ACCOMPLISHMENTS 

The Program obligated $1,922,015 from the CVPIA 

Restoration Fund to achieve the following:

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 

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 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, 

funds from the State of California, and funds from 

the CVPIA 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 

San Joaquin River Restoration 

Program

 Public Law 111-11
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

monitoring data. In FY 2013, 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 

2012 ATR in March 2013 and the Final 2013 MAP in 

November 2012.

Mendota Pool Bypass and Reach 2B 

Improvements Project – In FY 2013 and in support 

of the Restoration Goal, Reclamation funded ongoing 

work towards development of the Environmental 

Impact Statement/Environmental Impact Report for 

the Program’s Mendota Pool Bypass and Reach 2B 

Improvements Project. The Purpose of this project is 

to construct the Mendota Pool Bypass to convey flows 

at 4,500 cubic feet per second from River Reach 2B 

downstream to River Reach 3 and ensure fish passage 

downstream. 

The above accomplishments were achieved with 

CVPIA funding. To see all SJRRP accomplishments, visit 

www.restoresjr.net.

Trap and Haul Study on the San Joaquin River upstream of the Merced River confluence
ECOSYSTEM AND WATER SYSTEMS OPERATIONS MODELS 3406 (g) 45

FISHERIES

Delta outflow, (3) development of several baseline 

CalSim II models for the COA negotiations and the 

COA Agreement re-evaluations, (4) application of 

CalSim II model to study the feasibly of North Bay 

Aqueduct (NBA) Alternative Intake for EIR and EIS 

reports, (5) application of CalSim II model to study 

the feasibility of raising the dam of San Luis Reservoir 

and for seismic analysis, (6) modification of CalSim 

II model to evaluate the proposed flow standards in 

the San Joaquin Basin under the SWRCB’s “Review of 

the San Joaquin River Flow and Southern Delta Water 

Quality Objectives”, (7) modification of the CalSim 

II model to evaluate the SWRCB Supplemental 

Environmental Document and to evaluate proposals 

being made under the associated settlement process, 

(11) evaluation of new BDCP alternatives and (12) 

development of more user-friendly automated data 

processing packages for input/output analysis and 

display. These developments and 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 FY13 include (1) 

implementation of North Delta Diversion option (a.k.a. 

Isolated Facility), (2) development of a dynamic 

San Joaquin, (3) addition of an enlarged Shasta 

Dam option, and (4) addition of an enlarged Sisk 

Dam option. This involved developing WRESL code, 

corroborating results with CalSim II, and implementing 

the new options in the GUI.

CalSim 3.0 accomplishments for FY13 include (1) 

QA/QC of the model, calibration and validation 

of hydrology, and stabilization of the model for 

Sacramento Valley for the beta release, (2) updated 

precipitations from PRISM in the Sac valley, (3) 

updated land uses for current and future levels in 

the Sac valley, (4) refinement of the CalSim 3.0 

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 2013 ACCOMPLISHMENTS 

The Modeling Program obligated $863,020 from the 

Restoration Fund and $180,840 from the Water and 

Related Fund in FY13.

CalSim II accomplishments for FY13 include (1) 

modifications of CalSim II codes to use with new 

WRIMS2 engine and to develop the study results for 

the 2013 Delivery Reliability Report, (2) modifications 

of the CalSim II codes to incorporate the D1485, 

D1641, B2, and BO RPAs and then investigation of 

the effects of these regulations on water supply and 

Ecosystem and Water Systems 

Operations Models

 3406 (g)
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

FISHERIES

schematic/presentation tools, and (5) updated model 

debugging toolbox.

HEC-5Q based water temperature model 

accomplishments for FY13 include the addition of the 

American River and the Feather River.

C2VSIM (California Central Valley GroundwaterSurface Water Simulation Model) accomplishments 

for FY13 include (1) completion of C2VSIM final 

report for the historical simulation 1922-2009 and 

associated appendixes and released to the public in 

July, 2013, (2) holding a two day public workshop on 

the C2VSIM model in January 2013, (3) participation 

in the CWEMF Peer Review Public workshop on 

integrated hydrological models in April, 2013, (4) 

publication of a DWR-UC Berkeley joint paper on 

the impact of extended droughts on Central Valley 

water resources and cropping which appeared 

in the July-Sep issue (vol. 3 issue 3) of the British 

Journal of Environment and Climate Change, and (5) 

implementation of the San Joaquin portion of C2VSIM 

into CalSim 3.

ANN Model accomplishments for FY13 include 

incorporation of the turbidity estimation in the Delta 

channels.

DSM2 model accomplishments for FY13 include (1) 

recalibration of DSM2 version 8.1 for beta release, (2) 

improvement of applying DETAW to DSM2 Historical 

Simulation, (3) supporting Delta emergency response, 

(4) developing visualization tools to analyze effects 

of Delta Barriers on water quality, (5) updating the 

historical X2, and (6) adding fish behaviors to PTM 

module of DSM2.

inSALMO accomplishments for FY13 include (1) 

updating the model to versions inSALMO 1.5 and 

inSALMO-FA including developing user manuals 

and help files;, (2) publishing a report documenting 

model validation and calibration (Railsback, S. F., 

B.C. Harvey, and J. L. White; 2013), (3) organizing 

a 2-day training session on September 24-25 in 

Sacramento, CA; and (4) developing a document 

discussing recommendations for future developments 

and applications of inSALMO.

HydroGeoSphere (HGS) accomplishments for FY13 

include (1) calibration of the HydroGeoSphere (HGS) 

San Joaquin Valley model, (2) analysis of the sensitivity 

of land subsidence to different spatiotemporal 

distributions of groundwater pumping around the 

Delta-Mendota Canal (DMC), and (3) completion of a 

final report on the model’s development and possible 

application.

The 3406 (g) program also prepared publications 

and provided support to model applications for 

stakeholders. Table 13 presents the nine model types/

areas and FY13 accomplishments.

All of the projects that were undertaken in FY2013 met 

or exceeded the performance targets.

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
Chapter 3

CVP WATER 

OPERATIONS

RESOURCE 

AREA

Central Valley Project Improvemen
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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 Incremental 

Methodology (IFIM) studies, undertaken as part 

of Section (b)(1)(B), which identify optimal flow, 

temperature needs, and timing for the life stages of 

anadromous fish.

The Dedicated Yield Program (DYP) actions affecting 

fish fall into the following categories: 

•	Instream flow augmentations on CVP-controlled 

streams intended to protect salmon and 

steelhead, as well as contribute toward meeting 

Anadromous Fish Restoration Program (AFRP) 

Final Restoration Plan flow objectives

•	Increased releases from Goodwin Reservoir 

to help meet the Water Quality Control Plan 

(WQCP) requirements for San Joaquin River 

flows at Vernalis for fish and wildlife standards

•	Increased releases from Keswick and/or Nimbus 

reservoirs to help meet the WQCP fish and 

wildlife standards

•	Export reductions at the CVP Jones pumps to 

protect at-risk fish species, notably salmon, 

steelhead and delta smelt, and to help meet the 

WQCP Delta standards

PERFORMANCE MEASURES

Annual contribution – Reclamation annually 

contributes up to 800,000 AF of water from CVP 

facilities. In dry years, the target 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 2013 ACCOMPLISHMENTS 

The program obligated $551,887 from the Restoration 

Fund in FY 2013. 

The Water Year (WY) 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 largely determined by precipitation and 

is therefore indicative of local and regional conditions 

that influence climate, snowpack and runoff. 

WY 2013 started off much wetter than normal with 

October – December precipitation values ranging 

from 150-170% of the 15-year average and reservoir 

inflow values ranging from 100-180% of the 15-year 

Dedicated 800,000 acre-feet 

Project Yield

 3406 (b)(2)
DEDICATED 800,000 ACRE-FEET PROJECT YIELD 3406 (b)(2) 49

WATER OPS

average at CVP controlled reservoirs. The wet start 

was followed by the driest January – June period 

on record resulting in WY 2013 precipitation values 

ranging from 70-90% of the 15-year average and 

reservoir inflow values ranging from 50-70% of the 15-

year average at CVP controlled reservoirs. The final 

WY 2013 classification was Dry for the Sacramento 

Valley and Critical for the San Joaquin Valley. 

700,000 AF of (b)(2) water was available for fish 

actions in water year 2013. Table 14 presents the 

historic allocation and use of (b)(2) water. Specific 

uses for 2013 (b)(2) water was not available at the 

time of printing. 

This program activity partially funds 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, CDFW, and DWR, evaluate 

the data and collaboratively decide where to 

apply CVPIA (b)(2) water. Interior provides detailed 

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

cvo.

Table 14: Allocation Target and Use of (b)(2) Water, 2001-2013

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

2013 Dry 700,000 700,000

* 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.
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

WATER OPS

Keswick Dam Gate House
WATER ACQUISITION PROGRAM - INSTREAM WATER 3406 (b)(3) 51

WATER OPS

Related Fund. The Instream WAP used this funding for 

the availability and ability to use up to 25,000 acre 

feet of supplemental water to help meet the Vernalis 

spring flow target.

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.

Table 15 shows the instream water acquisitions from 

1994-2013.

The Instream Water Acquisition Program (Instream 

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. 

Water acquisition for CVPIA-designated refuges and 

wildlife management areas is discussed in Section 

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

(Refuge WAP).

PERFORMANCE MEASURE

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

800,000 AF dedicated from CVP yield to meet the 

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

CVPIA Final PEIS, Jan 2001).

FY 2013 ACCOMPLISHMENTS 

The Instream WAP obligated $2,940,055 from the 

Restoration Fund and $2,565,077 from the Water and 

Water Acquisition Program – 

Instream Water

 3406 (b)(3)
52 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

WATER OPS

Table 15: Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 

 1994-2013

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

2013 0 0

Average 74,646 37

Sunset at Yolo Bypass
FLOW FLUCTUATIONS AND RESERVOIR STORAGE 3406 (b)(9) & (19) 53

WATER OPS

FY 2013 ACCOMPLISHMENTS 

The FFP obligated $96,965 from the Restoration Fund 

in FY 2013. 

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 2012-2013 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.

Sacramento River – In coordination with the Golden 

Gate Salmon Association under their project B.11, 

Sacramento River Stranding, the agencies developed 

a project description, public draft Environmental 

Assessment, and a draft agreement to reduce incidents 

of fall Chinook salmon redd dewatering following the 

conclusion of irrigation season. Although biological 

conditions prevented implementation of the project in 

fall of calendar year 2013, the agencies will continue 

to prepare to implement the project in 2014.

American River –Three salmonid isolation pool 

surveys were conducted in January, March, and April 

of 2013 and multiple steelhead redd surveys took 

place December 2012 through April 2013. In the 

isolation pool surveys, a small number of steelhead 

and Chinook salmon were observed. No rescue 

measures were implemented. 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.

River and stream flow fluctuations can result in fish 

losses through 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 meet the 

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 end-of-September storage. These sets of 

actions broadly relate to the flow release schedule for 

Keswick Dam and Trinity Dam to maintain cold water 

supplies necessary for egg incubation for the following 

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

year type and amount of carryover storage at the end 

of September, the BO mandates close coordination 

between NMFS, California Department of Fish and 

Wildlife (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)
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

WATER OPS

Table 16: Carryover Storage at Shasta and Trinity Reservoirs, 1998-2013

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

2013 Dry 1.9 MAF 1,303 TAF

* million acre-feet

** thousand acre-feet

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. 

Carryover Storage

The RSP met the carryover targets for Shasta and 

Trinity reservoirs in FY 2013 with 1.906 MAF and 

1,303 TAF, respectively (see Table 16). 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.

Late afternoon view of Shasta Lake.
CONTRACT RENEWALS AND WATER TRANSFERS 3404 (c) and 3405 55

WATER OPS

The CVPIA authorizes and imposes terms on contract 

renewals and water transfers.

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, 100 long term renewal contracts and 28 

interim-renewal contracts have been executed within 

the various divisions of the CVP. 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. Long 

term execution of the interim-renewal contracts and the 

remaining unexpired contracts is pending completion 

of final biological opinions required to support 

operation of the CVP. 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, upon which time, Reclamation 

intends to complete long term contract renewal.

WATER TRANSFERS (3405)

Water transfers are a means by which water supplies 

under contract can be reallocated from one user to 

another on a short term or long term basis, to assist 

in meeting existing and future water needs within 

California. Water transfers create flexibility in the 

place and timing of water deliveries that sustain 

agriculture, municipal and industrial health and safety 

and provide environmental and recreational benefits. 

Section 3405 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 a total of 472,393 acrefeet of CVP water for transfer for FY 2013 : 

•	A total of 412,710 acre-feet of CVP agricultural 

water was approved for both agricultural and 

municipal & industrial (M&I) purposes;

•	A total of 40,183 acre-feet of CVP M&I water 

was approved for both agricultural and M&I 

purposes. 

Of the amount of water approved for transfer in 

FY2013, 19,500 acre-feet was made available to 

Reclamation’s Refuge Water Supply Program. 

Contract Renewals and Water 

Transfers

 3404 (c) & 3405
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

WATER OPS

Dos Amigos Pumping Plant
Central Valley Project Improvemen

Chapter 4

REFUGES

RESOURCE 

AREA
58 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

REFUGES

Refuge Water Supply Program

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

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, and construction of 

water delivery facilities.

• 3406 (d)(5) Refuge Facilities Construction 

Actions – Infrastructure construction to provide 

full Level 4 water supplies to the boundary of the 

CVPIA refuges. 

This component supports delivery of water to those 

lands identified in the Report on Refuge Water Supply 

Investigations (March 1989), and the San Joaquin 

Basin Action Plan/Kesterson Mitigation Action Plan 

(December 1989).

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

wetland habitat areas, hereinafter referred to as 

“refuges”, annually receive water of specified quantity, 

of suitable flow rate and timing, and suitable quality 

to support their wetland and aquatic environments. A 

total of 19 refuges are served by the program (shown 

in Figure 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 difference 

between Level 2 and Full Level 4 water supplies; 

it equals 133,264 AF.

Full Level 4 is the total annual amount of water 

identified for each refuge in CVPIA as required for 

optimum wetlands and wildlife habitat development 

and management. The Full Level 4 water delivery 

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

when Level 2 and Incremental Level 4 water targets 

are met in full. 

Each year, Reclamation strives to provide as 

much Incremental Level 4 water as possible. The 

CVPIA specifies that Reclamation must acquire this 

Incremental Level 4 water supply through voluntary 

measures such as water conservation, conjunctive use, 

purchase, lease, donation, or similar activities.

LONG-TERM SUPPLY 

CONTRACTS PROVIDE 

STABILITY FOR REFUGE 

OPERATORS

To ensure reliability for refuge managers, Reclamation 

entered into long-term water supply contracts with 

the three refuge managing agencies: CDFW, the 

Service, and Grassland Water District (GWD). These 
REFUGE WATER SUPPLY PROGRAM 3406 (d)(1), (2) & (5) 59

REFUGES

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 comprised 

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 

2013, 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 2013, 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.
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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
REFUGE WATER ACQUISITION 3406 (d)(2) 61

REFUGES

The Refuge Water Acquisition Program (RWAP) is 

responsible for the acquisition of 133,264 acrefeet (AF) of Incremental Level 4 Water (also called 

supplemental water) for critical wetland habitat 

supporting resident and migratory waterfowl, 

threatened and endangered species, and wetland 

dependent aquatic biota on the refuges.

Presently, Incremental Level 4 (IL4) water consists of 

annual purchases from willing sellers from both surface 

and groundwater supplies. In 1998 and 2005 the 

RWAP acquired a total of 9,300 AF of permanent 

IL4 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 IL4 water to 

refuge boundaries annually (i.e. 33,264 AF plus any 

additional water needed to cover conveyance losses), 

excluding replacement water.

FY 2013 ACCOMPLISHMENTS 

The RWAP obligated $5,250,711 from the Restoration 

Fund and $350,000 from the Bay-Delta Fund in FY 

2013. Funds were used for water purchases, ground 

water assessment, program administration and the 

South-of-Delta (SOD) coordinator.

The RWAP entered into contracts to purchase up to 

40,596 AF of IL4 water. This water was acquired 

for delivery in the 2013 water year, which covers 

a portion of calendar year 2013 and a portion of 

calendar year 2014 (March 1 – February 28). The 

up-to amount (40,596 AF) of purchased water was 

acquired from a variety of surface and ground water 

sources. In addition, permanent surface water of up 

to 9,300 AF and mitigation water of 2,500 AF were 

acquired at no cost and increased the up-to amount of 

IL4 to 52,396 AF, which includes water to account for 

conveyance losses such as seepage and evaporation 

(see Table 17). 

In fiscal year 2013 approximately 48,096 AF of IL4 

water was delivered to the refuges: 43,596 AF to 

nine SOD refuges and 4,000 AF to Delevan NWR, a 

North-of-Delta (NOD) refuge. See the next section on 

Conveyance for more information on water deliveries. 

Refuge Water Acquisition

 3406 (d)(2)
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

REFUGES

Table 17: Incremental Level 4 Acquisitions by Fiscal Year, 2002-2013

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

2013 52, 396 39

Average 63,833 47

* 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. 

Snow Geese: lit by a break in the fog...and preparing for a watery rest with landing gear deployed.
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 63

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 Incremental Level 4 (IL4) 

acquired water supplies by specified amounts to 

the refuges totaling 133,264 acre-feet.

The RWCC delivers L2 and IL4 water supplies to the 

refuges through agreements with water conveying 

entities. Established refuge allocations for L2 and IL4 

water supplies serve as the Program’s goals for water 

conveyance quantities. 

Reclamation entered into five long-term water supply 

contracts with GWD (1), the Service (2), and CDFW 

(2) 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 IL4 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 (includes 

26,007 AF of replacement water); and IL4 water of 

133,264 AF per year.

A portion of L2 water supplies is provided from 

non-CVP diverse sources, which assist in minimizing 

possible adverse effects on other CVP contractors.

FY 2013 ACCOMPLISHMENTS 

The program obligated $11,360,280 from the 

Restoration Fund.

Delivery – In 2013, an estimated 389,343 AF of L2 

water was delivered to the refuges, representing 92% 

of the target (Table 18).

Approximately 48,096 AF of IL4 water was delivered, 

representing 36% of the target. Table 19 shows the 

targets and deliveries for each refuge for the 2013 

Fiscal Year.

Diversification – Of the total of 389,343 AF of L2 

water delivered in 2013, a total of 51,879 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)
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

REFUGES

Fiscal 

Year* L2 Delivered

% 422,251 AF 

L2 Goal** Inc L4 Delivered

% 133,262 AF 

Inc L4 Goal*** Total Delivery

% Goal 

(555,515 AF)

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

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

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

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

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

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

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

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

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

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

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

2013 389,343 92 48,096 36 437,439 79

Average 

Deliveries

383,603 91 66,588 50 450,190 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 18: Level 2 (L2), Incremental Level 4 (Inc L4) and Full Level 4 Delivery Water by Year, 

2002-2013

Great Egret at Delevan NWR.
REFUGE WATER CONVEYANCE 3406 (d)(1), (2) & (5) 65

REFUGES

Table 19: Water Targets and Deliveries for Each Refuge (FY 2013)

WATER ALLOCATION TARGETS 2013 DELIVERIES % TARGET 

ACHIEVED***

Refuge Name - 

Region

Level 2 

Water (AF)*

IL4 Water 

(AF)**

Full level 4 

Water (AF) 

(= L2+IL4)

Level 2 

Water (AF)

IL4 Water 

(AF)

Total 

Delivered 

(AF) 

(= L2+IL4)

Level 2 

Water (%)

IL4 Water 

(%)

Grassland Water District (private) — San Joaquin Valley

Grassland RCD 125,000 55,000 180,000 133,281 25,552 158,833 107 46

CA Department of Fish and Wildlife — Sacramento Valley

Gray Lodge WA 35,400 8,600 44,000 29,959 0 29,959 85 0

CA Department of Fish and Wildlife — San Joaquin Valley

Volta WA 13,000 3,000 16,000 10,706 0 10,706 82 0

Los Banos WA 16,670 8,330 25,000 17,787 1,909 19,696 107 23

Salt Slough Unit 6,680 3,340 10,020 7,227 2,882 10,109 108 86

China Island Unit 6,967 3,483 10,450 4,488 2,760 7,248 64 79

Mendota WA 27,594 2,056 29,650 28,345 934 29,279 103 45

U.S. Fish and Wildlife Service — Sacramento Valley

Sacramento NWR 46,400 3,600 50,000 37,221 0 37,221 80 0

Delevan NWR 20,950 9,050 30,000 16,094 4,000 20,094 77 44

Colusa NWR 25,000 0 25,000 15,254 0 15,254 61 N/A

Sutter NWR 23,500 6,500 30,000 13,432 0 13,432 57 0

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

San Luis Unit 19,000 0 19,000 19,184 0 19,184 101 N/A

Kesterson Unit 10,000 0 10,000 9,539 0 9,539 95 N/A

West Bear Creek Unit 7,207 3,603 10,810 7,582 0 105 105 0

Freitas Unit 5,290 0 5,290 5,068 N/A 5,068 96 N/A

Merced NWR 13,500 2,500 16,000 12,644 2,500 15,144 94 100

East Bear Creek Unit 8,863 4,432 13,295 7,776 0 7,776 88 0

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

Kern NWR 9,950 15,050 25,000 12,976 7,559 20,535 130 50

Pixley NWR 1,280 4,720 6,000 780 0 780 61 0

TOTAL 422,251 133,264 555,515 389,343 48,096 437,439 92 36

* 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).
66 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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 Act. The RFCC 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 

Refuge Facilities Construction 

Component

 3406 (d)(5)

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.
REFUGE FACILITIES CONSTRUCTION AND SAN JOAQUIN BASIN ACTION PLAN LANDS 3406 (d)(5) 67

REFUGES

PERFORMANCE MEASURES 

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

refuges have the external conveyance capacity to 

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

an annual basis.

FY 2013 ACCOMPLISHMENTS 

In FY 2013, the RFCC obligated $31,985 from the 

Restoration Fund in support of refuges identified in the 

Plan. In addition, the RFCC obligated $9,583,686 

from the Restoration Fund in support of refuges 

identified in the Report. 

In FY 2013, the RFCC contracted for services to 

provide ongoing repairs to the East Bear Pumping 

Plant located at the East Bear Creek Unit of the San 

Luis National Wildlife Refuge. 

In FY 2013, the RFCC, in conjunction with the 

RWCC, completed modification of Gray Lodge and 

Pixley Groundwater Wells, which included Pixley 

NWR Alfalfa Valve Erosion Repairs; installation of 

transducers, timers and oil lube systems. 

A contract for a feasibility study was executed for 

the Sutter National Wildlife Refuge. The study is to 

assess both an interim solution and identify a long-term 

comprehensive solution for a permanent reliable water 

supply conveyance system. The study is expected to 

be completed in FY14.

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

of the Biggs-West Gridley Water District (BWGWD) 

Facilities Improvement Project will be completed by the 

end of 2013. Construction of this project is expected to 

commence in FY 2014. When completed, 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 20.

Dragonfly at Sacramento NWR.
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

REFUGES

Table 20: Target FL4 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 2016

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 1,280 21 2017
Central Valley Project Improvemen

Chapter 5

OTHER

RESOURCE 

AREA
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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

Since fiscal year 1996, the HRP has provided 

significant contributions by funding about 120 diverse 

and valuable projects to benefit a multitude of 

federally listed and other special status species that 

were impacted by the CVP. Federally listed species 

which have benefitted include the San Joaquin kit fox, 

giant kangaroo rat, riparian brush rabbit, blunt-nosed 

leopard lizard, giant garter snake, bay checkerspot 

butterfly, Lange’s metalmark butterfly, vernal pool plant 

and invertebrate species, and gabbro and serpentine 

soils species. The HRP provides leveraging of funds by 

attracting additional funding partners which decreases 

the amount of HRP funds needed to implement a 

project; partners have contributed about 85 percent of 

total project costs. Land acquisition projects currently 

have the highest priority and receive at least 50 

percent of the available funding. 

Protection and Restoration – The program 

contributes to the protection and restoration of 

threatened and endangered species habitats affected 

by the construction and operation of the CVP. 

Protection includes acquisition of lands through fee title 

or conservation easements. Since 1996, over 15,000 

acres have been acquired and restored with HRP 

funds (see Table 21). Various habitat types throughout 

the Central Valley have benefitted including alkali 

sink/scrub, valley grassland, riparian, vernal pools and 

other wetlands, serpentine soils, and chaparral.

The 1999 State Water Resources Control Board 

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

Reclamation provide compensation and habitat 

values to mitigate for impacts associated with the 

delivery of CVP water to lands previously outside the 

CVP Consolidated Place of Use. It identifies the HRP 

as one of three Reclamation programs suitable for 

fulfilling the mitigation plan. Pursuant to the SWRCB’s 

D-1641, Reclamation developed the Consolidated 

Place of Use, Habitat Mitigation Plan and Monitoring 

and Reporting Program (HMP) as a report/strategy 

of how the mitigation requirements will be addressed. 

The HMP identifies acquisition, maintenance, and 

restoration of 45,391 acres needing to occur as 

mitigation related to the CVP Consolidated Place of 

Use. To date, the program has protected and restored 

954 acres within the CVP Consolidated Place of Use.

Research and Captive Propagation and 

Reintroduction – The program also supports the 

recovery of threatened and endangered species 

through stabilization and improvement of species 

populations by funding research and captive 

propagation and reintroduction activities. In part, 

research projects ultimately contribute important 

information towards increasing current and future 

protection and/or restoration of species or habitats 

impacted by the CVP. Research has included vernal 

pool mapping, assessing the potential for listed species 

reintroductions, and numerous genetics analyses. 

Captive propagation and reintroduction have 

benefitted two critically endangered species as well as 

other federally listed species.

Habitat Restoration Program

 3406 (b)(1) “Other”
HABITAT RESTORATION PROGRAM 3406 (b)(1) “Other” 71

HABITAT

FY 2013 ACCOMPLISHMENTS 

In 2013, $1,604,246 was allocated to the program 

from the Restoration Fund to achieve the following: 

Protection and/or Restoration – The HRP funding 

helped protect 1,953 acres of land through fee title 

acquisitions of 76 acres of vernal pools habitat in Butte 

County; 1,552 acres of grassland habitat in Fresno 

County; and 325 acres of scrub-shrub habitat in 

Tulare County. (See Table 21 for approximate acres 

protected and restored from 1996 through 2013 using 

HRP funds). One thousand eight hundred and seventyseven of these acres also count towards the SWRCB’s 

D-1641 requirements.

Other Activities – The HRP provided funds for one 

research project to develop the definitive and requisite 

data on population genetic structure to help develop 

and guide management options for the endangered 

riparian brush rabbit in San Joaquin County. 

Year

Acreage 

Protected

Acreage 

Restored

Cumulative 

Acreage 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

2013 1,953 0 15,262

Total 12,247 3,938 16,185

Table 21: Approximate Acres of Habitat 

Protected and Restored by the (b)(1) “Other” 

Program, 1996-2013, using HRP Funds

Giant Kangaroo Rat habitat protected in the Ciervo Hills of 

western Fresno County.

Riparian brush rabbit with Kim Forrest USFWS

Photo: U.S. Fish & Wildlife Service
72 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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.

The LRP will complete land acquisition and restoration 

at the Atwell Island site in 2014. This site will be 

transferred to BLM for management and the program 

will not receive CVPIA Restoration funds after this 

transaction.

FY2013 ACCOMPLISHMENTS 

The program obligated $500,000 from the 

Restoration Fund, and $47,000 from the Water and 

Related Resources Fund. 

Retire agricultural land – Over 9,300 acres of 

drainage impaired land have been acquired to 

date from willing sellers for the Land Retirement 

Demonstration Project (LRDP). Contacts with the 

multiple land owners were made for the acquisition of 

the remaining 750 acres at the Atwell Island project. 

However, no land was acquired from willing sellers 

by the program during FY 2013. Table 22 lists the 

cumulative accomplishments of land retirement and the 

annual restoration and agricultural drainage reduction 

accomplishments.

Restore Habitat – 5,900 pounds of locally grown 

seed from desert adapted salt tolerant native plant 

species were planted on 197 acres of previously 

acquired land at the Atwell Island site in fiscal year 

2013. A good response of annual flora was observed 

at one restoration site in the spring of FY 2013 and a 

fair response in another, contributing to the ongoing 

restoration of alkali sink habitat at the site.

Reduce agricultural drainage volume – The 

program reduced the amount of agricultural drainage 

water on LRDP lands by approximately 3,600 acrefeet in FY 2013. Cumulative drainage reduction 

estimates were revised based on LRDP land use data 

provided by BLM.

Land Retirement Program

 3408 (h)
LAND RETIREMENT PROGRAM 3408 (h) 73

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 2,962

2005 625 0 349 3,275

2006 38 0 416 3,275

2007 213 0 475 3,275

2008 0 0 390 3,275

2009 0 0 380 3,275

2010 50 0 400 3,320

2011 0 0 260 3,361

2012 0 0 260 3,465

2013 0 0 197 3,585

Total 7,266 2,090 6,868 44,220** 

 * 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 1995-2013.

Table 22: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2013
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

HABITAT

Successful restoration of annuals at Atwell Island.
CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS 75

Central Valley Project Improvemen

CHAPTER 6

PROGRESS TO DATE

TOWARD CVPIA

ACCOMPLISHMENTS
76 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Performance Goal Description Target

Reporting 

Period

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2013 

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 - 2012 

average

356,780 48 293,985

Double the number of naturally produced, 

Central Valley wide, Late Fall-run Chinook

68,000 fish 1992 - 2012 

average

17,218 25 5,539

Double the number of naturally produced, 

Central Valley wide, Winter-run Chinook

110,000 fish 1992 - 2012 

average

6,191 6 3,900

Double the number of naturally produced, 

Central Valley wide, Spring-run Chinook

68,000 fish 1992 - 2012 

average

18,397 27 30,522

Double the number of Central Valley wide 

Green Sturgeon

2,000 fish 1992 - 2009 

average

2,948 147 10,272 Last data submission was 2009

Double the number of Central Valley wide 

15-year old, White Sturgeon

11,000 fish 1992 - 2009 

average

6,237 57 6,258 Last data submission was 2009

Double the number of Central Valley wide 

Striped Bass

2,500,000 fish 1992 - 2011 

average

964,033 39 894,606 Data from 2011

Double the number of Central Valley wide 

American Shad

4,300 fish 1992-2011 

average

2,389 56 892 Data from 2011

Cubic Yards of Spawning gravel placed in 

the American, Merced, and/or Tuolumne 

rivers.

unspecified Annual N/A N/A 55,496

Complete 105 structural actions 105 actions Cumulative 72 68 6 Caprini Low Flow Crossing Fish 

Passage Project was completed

Contribute towards completion of 128 High 

and Medium Priority Actions

128 actions Cumulative 46 36 0

DEDICATED PROJECT YIELD, 3406 (b)(2)

Provide instream flow, specified based on 

Wet, Dry, or Critically Dry year.

Dry Year target is 

700,000 acre-feet

Annual N/A 100 700,000 2013 Water Year was classified 

Dry

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 and 

Rating Tool or PART) and program-defined goals. 

Listed below are goals by program for ongoing 

programs. The 2013 Accomplishment status is 

based upon the specific FY 2013 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 77

Performance Goal Description Target

Reporting 

Period

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2013 

Accomplishments Comments

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

Provide supplemental (b)(2) instream flow 

water

200,000 acre-feet Average 

from 1994 - 

2013

74,646 0 0

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

CLEAR CREEK RESTORATION, 3406 (b)(12)

Restore stream channel 2 miles Cumulative 1.5 75 0

Place spawning gravel annually 25,000 tons (1) Annual N/A 0 0

Meet variable flow target Variable (cfs) Annual N/A 100 200 Ongoing operation

Maintain water temperature for optimum 

anadromous fish production

Maintain proper 

temperature 

100% of the time

Annual N/A 100

96

100% for 60°F 1-Jun to 14-Sep

96% for 56°F 15-Sep to 31-Oct

2012 data

SPAWNING GRAVEL, 3406 (b)(13)

Place 10,000 tons of spawning gravel 

annually in the Sacramento River.

10,000 tons Annual N/A 140 14,000

Place 3,000 tons of spawning gravel 

annually in the Stanislaus River

3,000 tons Annual N/A 0 0

Place 7,000 tons of spawning gravel 

annually in the American River

7,000 tons Annual N/A 87 6,000

Increase the percentage of spawning 

salmonids using placed gravel in the 

Sacramento River

25% usage Annual N/A 304 76%

Increase the percentage of spawning 

salmonids using placed gravel in the 

Stanislaus River

10% usage Annual N/A 280 28%

Increase the density of redds on emplaced 

gravel in the American River

0.03 redds/sq. 

meter

Annual N/A 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 41 Undefined 6

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 2013 data not available until 

January 2013

Increase the escapment of Naturally 

produced Fall-run Chinook Salmon

62,000 fish 1992 - 2012 

Average

16,110 85 52,687 2013 data not available until 

January 2013

Increase the escapment of Hatchery 

produced Spring-run Chinook Salmon

3,000 fish 1992 - 2012 

Average

8,918 224 6,712 2013 data not available until 

January 2013

Increase the escapment of Naturally 

produced Spring-run Chinook Salmon

6,00 fish 1992 - 2012 

Average

6,079 296 17,730 2013 data not available until 

January 2013

Increase the escapment of Hatchery 

produced Coho Salmon

2,100 fish 1992 - 2012 

Average

11,566 350 7,356 2013 data not available until 

January 2013

Increase the escapment of Naturally 

produced Coho Salmon

1,400 fish 1992 - 2012 

Average

1,890 567 7,939 2013 data not available until 

January 2013

Increase the escapment of Hatchery 

produced Steelhead

10,000 fish 1992 - 2012 

Average

12,347 57 5,737 2013 data not available until 

January 2013

Increase the escapment of Naturally 

produced Steelhead

40,000 fish 1992 - 2012 

Average

4,851 37 14,666 2013 data not available until 

January 2013

Improve Infrastructure to allow ROD flows 

(369 TAF - 815 TAF)

Unspecified Annual Within target 100
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Performance Goal Description Target

Reporting 

Period

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2013 

Accomplishments Comments

Provide minimum annual flows. The 

program releases between 369,000 and 

815,000 AF each year, in accordance with 

the ROD

453,000 Annual N/A 100 453,000 Based on 2013 as a dry 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 30 64 2

Place 10,000 cubic yards of coarse 

sediment annually

10,000 cubic 

yards

Annual N/A 17 1,700

Reduce fine sediment delivery from 

tributary watersheds

10,000 to 20,000 

cubic yards

Annual N/A 78-155 15,500

SAN JOAQUIN RIVER RESTORATION PLAN (SJRRP), 3406 (c) (1)

Reduce or avoid water supply impacts to 

Friant Division long-term contractors

Unspecified Annual 0 Undefined 0

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 modeltypes

Cumulative 8 89 0 (2)

CVP WATER OPERATIONS

RESERVOIR STORAGE, 3406 (b)(19)

Maintain minimum reservoir storage in 

Shasta Reservoir

19 MAF Cumulative 14 of 16 88 1.9 MAF

Maintain minimum reservoir storage in 

Trinity Reservoir

600 TAF Cumulative 16 of 16 100 1,303 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 39 52,396

REFUGE WATER SUPPLY PROGRAM - CONVEYANCE, 3406 (d)(1) & (d) (2)

Provide Level 2 water supplies 422,251 acre-feet Annual N/A 92 389,343

Provide incremental Level 4 water supplies 133,264 acre-feet Annual N/A 36 48,096 Full L4 delivery = 437,439 (79% 

goal)

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 491,145 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

OTHER

HABITAT RESTORATION, 3406 (b)(1) Other

Protect and/or restore habitat impacted by 

the CVP

Unspecified Cumulative 16,185 N/A 1,953

Protect and/or restore habitat areas 

specified by the SWRCB Decision 1641

45,391 acres Cumulative 10,929 20 1,877

LAND RETIREMENT, 3408(h)

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

1995–2013

 7,266 91 0
CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS 79

Performance Goal Description Target

Reporting 

Period

(Annual, 

Cumulative, 

or Average)

To Date

(Cumulative 

or Average)

% of 

Target

2013 

Accomplishments Comments

Retire 7,000 acres of Tranquility land Complete Cumulative, 

1995–2013

7,000 100 N/A

Restore 400 acres of retired land annually 400 acres Cumulative, 

1995–2013

6,868 76 197

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, 

1995–2013

44,220 60 104

(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.

(2) The Modeling Program is reviewing procedures to provide a more comprehensive reporting metric. A new metric may be in place for FY 2014.

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

Red Bluff Diversion Dam, 3406(b)(10) Complete

APPENDICES 81

Central Valley Project Improvemen

APPENDICES
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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 

cfs cubic feet per second

CPAR CVPIA Program Activity Review Report

CVP Central Valley Project

CVPIA Central Valley Project Improvement Act

CY Contract year

DHCCP Delta Habitat Conservation and Conveyance 

Program

DOI Department of the Interior

DWR Department of Water Resources

ECOSIM Ecology Cogent Operations Suite 

of Integrated Models

EDT Ecosystem Diagnostic and Treatment

EIR Environmental Impact Report

EIS Environmental Impact Statement

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 District

GWD Grassland Water District

HGS HydroGeoSphere

HRP Habitat Restoration Program

IFIM Instream Flow Incremental Methodology

Interior Department of the Interior

IP Implementation Plan

IRWMT Interagency Refuge Water Management

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 Impact

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

SDM structured decision making

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

USBR Bureau of Reclamation

Appendix A: Acronyms
APPENDIX B: GLOSSARY OF TERMS 83

• 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 

• 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 the 

Central Valley Project 

d. Increase water-related benefits provided 

by the Central Valley Project to the State 

of California through expanded use of 

voluntary water transfers and improved water 

conservation 

e. Contribute to the State of California’s interim 

and long-term efforts to protect the San 

Francisco Bay/Sacramento-San Joaquin 

Delta Estuary 

f. Achieve a reasonable balance among 

competing demands for use of Central Valley 

Project water, including the requirements of 

fish and wildlife, agricultural, municipal and 

industrial and power contractors

Appendix B: Glossary of Terms
84 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

• 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”

• Outcome

The intended results or consequences to be 

achieved through implementing measures and 

programs described in the CVPIA 
APPENDIX B: GLOSSARY OF TERMS 85

• 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 Project 

when available and acquired from willing sellers. 

Replacement water is delivered in addition to the 

Level 2 amounts specified in the CVPIA

• 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
86 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

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...”

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...”
APPENDIX C: CVPIA TITLE 34 OF PUBLIC LAW 102-575 87

Water Acquisition Program - Instream 

Water – Sections 3406 (b)(3) 

“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.”

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.”

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...”

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.”
88 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

Refuge Water Supply Program 

– Section 3406 (d)(1), 3406 (d)(2), 

3406 (d)(5)

“3406 (d)(1)Upon enactment of this title, the quantity 

and delivery schedules of water measured at the 

boundaries of each wetland habitat area described 

in this paragraph shall be in accordance with Level 2 

of the “Dependable Water Supply Needs” table for 

those habitat areas as set forth in the Refuge Water 

Supply Report and two-thirds of the water supply 

needed for full habitat development for those habitat 

areas identified in the “San Joaquin Basin Action 

Plan/Kesterson Mitigation Action Plan Report...”

“3406 (d)(2) Not later than ten years after enactment 

of this title, the quantity and delivery schedules of 

water measured at the boundaries of each wetland 

habitat area described in this paragraph shall be in 

accordance with Level 4 of the “Dependable Water 

Supply Needs” table for those habitat areas as set 

forth in the “Refuge Water Supply Report” and the 

full water supply needed for full habitat development 

for those habitat areas identified in the “San Joaquin 

Basin Action Plan/Kesterson Mitigation Action Plan 

Report...”

“3406 (d)(5) The Secretary is authorized and 

directed to construct or to acquire from non-Federal 

entities such water conveyance facilities, conveyance 

capacity, and wells as are necessary to implement 

the requirements of this subsection; provided, that 

such authorization shall not extend to conveyance 

facilities in or around the Sacramento-San Joaquin 

Delta Estuary...”

Ecosystem and Water Systems 

Operations Models – Section 3406 (g)

“The Secretary, in cooperation with the State of 

California and other relevant interests and experts, 

shall develop readily usable and broadly available 

models and supporting data to evaluate the ecologic 

and hydrologic effects of existing and alternative 

operations of public and private water facilities and 

systems in the Sacramento, San Joaquin, and Trinity 

River watersheds. The primary purpose of this effort 

shall be to support the Secretary’s efforts in fulfilling 

the requirements of this title through improved 

scientific understanding concerning, but not limited 

to, the following:

(1) a comprehensive water budget of surface and 

groundwater supplies, considering all sources 

of inflow and outflow available over extended 

periods;

(2) related water quality conditions and improvement 

alternatives, including improved temperature 

prediction capabilities as they relate to storage;

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

(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.”

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.”
APPENDIX D: MAPS 89

Appendix D: Maps

Central Valley Project (CVP) Service Area Boundary
90 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Trinity River Watershed

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APPENDIX D: MAPS 91

2013 CVPIA Accomplishments - Sacramento River, Lower Cow Creek & Lower Clear Creek Watershed

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92 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Cottonwood Creek Watershed

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APPENDIX D: MAPS 93

2013 CVPIA Accomplishments - Lower Yuba River Watershed ! Anadromous Fish Restoration Program Yuba River Hammon Bar Riparian Habitat Restoration 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 Y u b a 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 Y u b a R i v e r W a t e r s h e d

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94 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Lower Feather 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 F e a t h e r 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 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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Sacramento River
APPENDIX D: MAPS 95

2013 CVPIA Accomplishments - Upper Sacramento River Mainstem Watershed

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96 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Lower American River Watershed

! !

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Comprehensive Assessment and Monitoring Program

Constant Fractional Marking Program at Nimbus Fish Hatchery

Comprehensive Assessment and Monitoring Program

American River Rotary Screw Trap

Spawning Gravel and Anadromous Fish Restoration Program

Gravel placement & side channel at River Bend Park

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 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 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 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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APPENDIX D: MAPS 97

2013 CVPIA Accomplishments - Lower Sacramento 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 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 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 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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98 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Lower Calaveras 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 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 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 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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APPENDIX D: MAPS 99

2013 CVPIA Accomplishments - San Joaquin River - Delta Watershed

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100 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Lower Stanislaus River Watershed

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APPENDIX D: MAPS 101

2013 CVPIA Accomplishments - Upper Los Gatos Creek 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 - 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 3 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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102 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Middle San Joaquin River - Lower Merced Watershed

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APPENDIX D: MAPS 103

2013 CVPIA Accomplishments - Middle San Joaquin River - Lower Chowchilla Watershed

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104 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2013 ANNUAL REPORT

2013 CVPIA Accomplishments - Tulare - Buena Vista Lakes Watershed

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