Attachment_9-Battle_Creek_Restoration_Proj__Adaptive_Management_Plan.pdf

DRAFT

BATTLE CREEK SALMON AND

STEELHEAD RESTORATION PROJECT

ADAPTIVE MANAGEMENT PLAN

U.S. Bureau of Reclamation

Pacific Gas and Electric Company

National Marine Fisheries Service

U.S. Fish and Wildlife Service

California Department of Fish and Game

April 2004

DRAFT

BATTLE CREEK SALMON AND

STEELHEAD RESTORATION PROJECT

ADAPTIVE MANAGEMENT PLAN

Prepared for the

U.S. Bureau of Reclamation

Pacific Gas and Electric Company

National Marine Fisheries Service

U.S. Fish and Wildlife Service

California Department of Fish and Game

Prepared by

Terraqua, Inc.

Wauconda, Washington

April 2004

Adaptive Management Plan (Reconceived) Acknowledgements

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 i

ACKNOWLEDGEMENTS

This Adaptive Management Plan was prepared under the direction of the Adaptive Management Parties (Pacific Gas and Electric Company, California Department of Fish and Game, U.S. Fish and Wildlife Service, and National Marine Fisheries Service) by Terraqua, Inc., under subcontract to the U.S. Bureau of Reclamation using funding provided by California Bay- Delta Authority. Significant contributions to this document were provided by the Adaptive Management Parties, Stillwater Sciences, Jones and Stokes Associates, The Nature Conservancy, Kier Associates, and Navigant Consulting. Two scientific Technical Panels established by California Bay-Delta Authority provided important comments regarding adaptive management theory and practice which prompted substantial reconception of earlier drafts. Members of the Battle Creek Working Group provided reviews and additional policy suggestions.

Adaptive Management Plan (Reconceived) Notes to the Reader

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 ii

NOTES TO THE READER

This Adaptive Management Plan assigns specific meanings and definitions to some common words or proper nouns. Words used in the text that represent specific meanings as defined within this plan are indicated by capitalizing the first letter of each word. Definitions for these words can be found beginning on page III.D.1.

Table 1. A list of acronyms used within this report.

AFRP Anadromous Fish Restoration Program AMF Adaptive Management Fund AMP Adaptive Management Plan AMPT Adaptive Management Policy Team AMTT Adaptive Management Technical Team BCWC Battle Creek Watershed Conservancy BCWG Battle Creek Working Group BLM United States Bureau of Land Management CALFED CALFED Bay-Delta Program CAMP Comprehensive Assessment and Monitoring Program CBDA California Bay-Delta Authority CEC California Energy Commission CEQA California Environmental Quality Act CDFG California Department of Fish and Game CDWR California Department of Water Resources cfs Cubic Feet per Second CMARP Comprehensive Monitoring, Assessment, and Research Program CNFH Coleman National Fish Hatchery CNFH-AMP Coleman National Fish Hatchery Adaptive Management Program CRR Cohort Replacement Rate CVPIA Central Valley Project Improvement Act EPA Environmental Protection Agency ESA Endangered Species Act FERC Federal Energy Regulatory Commission IFIM Instream Flow Incremental Methodology MOU Memorandum of Understanding NEPA National Environmental Policy Act NOAA Fisheries National Marine Fisheries Service PG&E Pacific Gas and Electric Company PHABSIM Physical Habitat Simulation POC Point of Contact SNTEMP Stream Network Temperature Model TNC The Nature Conservancy TRPA Thomas R. Payne Associates USBR United States Bureau of Reclamation USFS United States Forest Service USFWS United States Fish and Wildlife Service WAF Water Acquisition Fund WUA Weighted Usable Area

Adaptive Management Plan (Reconceived) Public Involvement

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 iii

PUBLIC INVOLVEMENT

The public is invited to participate in the implementation of this Adaptive Management Plan (AMP). While many lay readers may find this AMP to be dry and technical in many cases, opportunities for public involvement are built into adaptive management throughout this document. This section highlights some of the ways that the public may be involved with adaptive management in Battle Creek and points to specific sections of the document for more information. Figure 1 illustrates some of the relationships between adaptive management and public involvement. Figure 2 provides a general illustration of the complex restoration activities in Battle Creek.

• The development of the Battle Creek Salmon and Steelhead Restoration Project and this AMP were done with full public participation in accordance with all public laws and regulations. The implementation of the Restoration Project and AMP will continue to be open to the public.

• Adaptive management in Battle Creek will involve extensive field studies and monitoring. Any adaptive management activities on private lands must meet strict performance protocols. See Section III.D.6 for details.

• All data collected during adaptive management monitoring will be made available to the public by dissemination to the appropriate agency information storage systems and an information system operated and maintained by the Battle Creek Watershed Conservancy (BCWC). An important exception, designed to protect the privacy of private landowners, involves incidental observations. Section III.D.6 states, in regards to monitoring on private lands, that “Field personnel will record only data that meets the purpose of the visit.

Incidental observations will not be recorded or shared with the public, but may be shared with the landowner upon request at any time. Field personnel will not discuss specifics of data collected from private properties with anyone outside of the staff designated by the AMP data management protocols.”

• Most monitoring activities will be funded through public funding sources (with the exception of those activities funded by the hydroelectric project Licensee). The public is invited to participate in decision making related to these public funding sources. See Section

III.D.4.

• All technical and decision-making meetings will be open to the public. In most cases, adaptive management meetings will be formally announced at least one month in advance.

Exceptions to this announcement procedure may occur in the case of emergencies when ad hoc meetings may be scheduled. In any case, the public is welcome to attend. See Section III.D.8 for details on meeting schedules and process.

• Any person requesting notification of adaptive management meetings will be provided with such notice. See Section III.D.8 for details.

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 iv

• Local landowners, watershed residents, and other members of the BCWC are given special recognition within this document. While these people may be fortunate to benefit most directly from restored salmon and steelhead populations in their own watershed, and from learning opportunities afforded by the project to local schools and residents, they also have unique burdens that come with the high level of monitoring activities within their watershed. Section 0 discusses the unique role of the BCWC in adaptive management.

• Local landowners, watershed residents, and other members of the public have an opportunity to participate in discussion of watershed issues within Battle Creek through participation in the Greater Battle Creek Working Group. The Greater Battle Creek Watershed Working Group provides an open forum for coordinating adaptive management activities among various entities.

Research Invitation

Scientific reviewers of the Battle Creek Salmon and Steelhead Restoration Project have recognized that the Restoration Project is an “extremely important opportunity” to learn about the value of many salmon restoration activities and how similar activities could benefit the restoration of other fish populations in California and the Pacific Northwest. Every effort should be made to guarantee that we learn from this valuable opportunity. Independent researchers are invited to participate in the learning opportunities inherent in this project. Interested researchers are encouraged to coordinate with the Adaptive Management Policy Team to explore opportunities for research in Battle Creek. All research in Battle Creek must follow appropriate laws and regulations, including permitting, and must observe the rights of private property owners. Interested researchers are encouraged to adhere to protocols described in Section III.D.6 regarding research on private property.

Document Road Map

The table of contents, list of figures, and list of tables are handy ways to understand the layout of this document. Section I.G provides additional detail on this document’s organization.

The reader interested in skimming the highlights of this AMP may wish to skip to the following AMP features:

• Conceptual Models (Conceptual Models 1, 2, and 3) page 8

• Uncertainties Table (Table 3) page 12

• Adaptive Management Objectives (Section III.A) page 41

• Monitoring Activities (schedule and budget) (Table 24) page 84

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 v

Figure 1. Institutional and funding relationships described in the Battle Creek AMP with related watershed restoration programs and community involvement.

Restoration Project Implementation

• Project Construction

• Construction Mitigation and

Monitoring

(Construction Fund)

Transfer/Startup Testing

Battle Creek Watershed Community Involvement

• B.C. Watershed

Conservancy

• Greater B.C. Working

Group

Coleman National Fish Hatchery

Sacramento River Watershed

• Ecosystem Approach

• CAMP

• CALFED Science Program

• CVPIA

• (Agency Funds, CVPIA and

CALFED funds)

Restoration Project Adaptive Management Plan

• Biological Monitoring

• Effectiveness

• Facility Monitoring

(Packard Foundation AMF, CALFED Water Acquisition Fund)

CALFED

$1 million Monitoring Fund

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 vi

Figure 2. Schematic of the relationship of the AMP and Adaptive Management objectives with other Restoration Project and non-project restoration activities that may affect salmon and steelhead in Battle Creek.

Mem orandum of U nders tanding

Contruc tion Monitoring

Adaptive M anagem ent Plan

Fac ilities Transfer Agreement

Facilit ies M onitoring Plan

Fac ilit ies Op eration and Maintenance Plan

Passage Objec tives

Gravel management at exist ing dam s

Linkages

Populat ion Object ives

Habitat Object ives

Non-Projec t R estoration Program s

In Bat tle C reek

Prop osed fisheries m anagem ent plan for upper Sacram ento R iver and tributaries

Proposed C olem an Powerhouse tailrace barrier

C olem an Nation al Fish Hatchery water supply modificat ions

Coleman National F ish Hatchery barrier dam m odifications

Coleman National F ish Hatchery Hatchery and Genetic Management Plan

C ALFED Ecosystem Restorat ion Program

Central Valley Project Improvem ent Ac t

R ecovery plans: threatened / endangered spec ies

Upper Sacram ento River Fisheries and Riparian H abitat Managem ent Plan

Steelhead Res toration and Management Plan

D elta and Sacram ento River Operat ions and Monitoring

Reference W atersheds

U.S. Forest Service

Batt le Creek Salmon and Steelhead Restorat ion

Program

U.S. Bureau of Land M anagem ent

Region al R estoration Program s

Non-Projec t Restorat ion Emergencies

Restoring Central Valley Streams:Plan for Act ion

Local com mu nity part icipat ion

Sediment quality m onitoring Batt le Creek W atersh ed Conservancy

Adapt ive Managem ent

Object ives

W atershed assessment

W ater tem perature and c limate monitoring

Data m anagem ent and d issem inat ion

Conservat ion easements and water rights

Sacram ento Corrid or H abitat Restorat ion Assessment

FERC Licen se Am m endm ent for FERC Projec t No. 1121

Coleman National F ish Hatchery Adaptive Managem ent Plan

Environm ental Impact Statem ent/ Env ironm ental Imp ac t Report

Act ion Specific Im plementat ion Plan

C entral ValleySalm on and Steelhead Restorat ion and Enhancement Plan

Pac ific Fisheries Managem ent Counc il and California Fish and Game C omm iss ion

Adaptive Management Plan (Reconceived) Preface

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 vii

PREFACE

Battle Creek has historically been regarded as a uniquely important salmon-producing watershed because of the large numbers and broad diversity of Chinook salmon and steelhead that have historically used this stream. The importance of restoring the fish habitat and populations within Battle Creek has long been recognized, but the urgency of the ongoing Battle Creek Salmon and Steelhead Restoration Project is heightened by the fact that this watershed is home to winter-run Chinook salmon, spring-run Chinook salmon, and steelhead, all of which are in danger of or threatened with extinction as defined by the federal Endangered Species Act (ESA). Furthermore, Battle Creek provides the only remaining accessible habitat in the Sacramento River watershed, other than the Sacramento River itself, that may be suitable for populations of winter-run Chinook salmon.

The primary goal of the Restoration Project is to restore and enhance about 42 miles of anadromous fish habitat in Battle Creek and an additional 6 miles of habitat in its tributaries while minimizing the loss of renewable energy produced by the Battle Creek Hydroelectric Project. The Restoration Project has been the result of a long planning process that culminated in a Memorandum of Understanding (MOU) between the Resource Agencies and Pacific Gas and Electric Company (PG&E). An integral part of the MOU was the direction to develop and implement an adaptive management program to monitor the effectiveness of restoration actions taken and make further adjustments to Hydroelectric Project facilities or operations as appropriate in pursuit of the primary goal of the Restoration Project.

Therefore, this document is the strategic plan agreed upon by the Resource Agencies and PG&E. Its goal is to implement specific actions to protect, restore, enhance, and monitor salmonid habitat at the Hydroelectric Project to guard against false attraction of Chinook salmon and steelhead, and to ensure that these fish in all life stages are able to fully access and beneficially use available habitat, thereby maximizing natural production and the full use of ecosystem carrying capacity. While this Plan was written primarily to conform to provisions of the MOU, it is also recognized that this Plan may assist the Federal Energy Regulatory Commission (FERC) regulating license compliance and may be incorporated as part of, or at least linked to, other Battle Creek watershed and statewide resource management efforts.

Because this plan is intended specifically to apply to the Restoration Project and is not a general watershed management plan, its objectives and protocols must be evaluated in light of these stated purposes.

Adaptive Management Plan (Reconceived) Executive Summary

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 viii

EXECUTIVE SUMMARY

The Battle Creek Salmon and Steelhead Restoration Project is a joint effort between PG&E, the National Marine Fisheries Service (NOAA Fisheries), California Department of Fish and Game (CDFG), U.S. Fish and Wildlife Service (USFWS), and U.S. Bureau of Reclamation (USBR) to restore salmon and steelhead runs in the Battle Creek watershed while maintaining the renewable energy production of the Battle Creek Hydroelectric Project (FERC Project No.

1121). A MOU was adopted in June 1999 stating the intent of the MOU Parties to engage in a restoration effort that would modify the facilities and operations of FERC Project No. 1121. The objectives of the Restoration Project are (1) the restoration of self-sustaining populations of Chinook salmon and steelhead and their habitat in the Battle Creek watershed, (2) up-front certainty regarding specific restoration components, (3) timely implementation and completion of restoration activities, and (4) joint development and implementation of a long-term AMP with dedicated funding sources to ensure the continued success of restoration efforts under this partnership.

The MOU identifies Adaptive Management as an important component of the Restoration Project (Figure 1). Adaptive Management uses extensive monitoring to identify problems, examine possible solutions for meeting the biological objectives, and if needed, allow changes to Contemporary strategies and actions within established limits to try to achieve the objectives and desired results. The Adaptive Management concept was formalized in this AMP developed by the PG&E, NOAA Fisheries, USFWS, and CDFG (collectively known herein as the “Parties”). Funding for implementation of the AMP is provided by the CALFED Monitoring Fund, the Water Acquisition Fund (WAF), the Adaptive Management Fund (AMF), and Licensee (PG&E).

The AMP provides guidance on implementing the Adaptive Management provisions of the MOU, and is intended to be consistent with the terms of the MOU. Any cases where the language in the AMP may conflict with the language in the MOU represent an oversight in the AMP. Therefore, the MOU prevails in any discrepancy that may be discovered between the AMP and the MOU.

The AMP was developed by Consensus between the Parties under the Adaptive Management Policy Team (AMPT) and the Adaptive Management Technical Team (AMTT).

The AMPT consists of management-level representation from each of the Resource Agencies and the Licensee and is authorized to make all final decisions regarding the implementation of the AMP and to provide policy direction and dispute resolution on issues forwarded to it by the AMTT. The AMTT consists of technical experts from each of the Resource Agencies and the Licensee and is responsible for the development and implementation of the AMP portion of the Restoration Project when it has been approved by FERC. Definitions are provided in the AMP to minimize confusion and to simplify the text. Words or phrases defined in the AMP appear capitalized within this plan.

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 ix

PROBLEM ESTABLISH ECOSYSTEM

GOALS/OBJECTIVES

SPECIFY

CONCEPTUAL

MODELS

Explore Policy Alternatives And Information Value Using Simple Simulations

INITIATE

RESTORATION

ACTIONS

Undertake Targeted Research

Undertake Pilot/Demonstration Projects

Implement Large Scale Restoration

Information

Learning

ASSESS

EVALUATE

ADAPT

Reassess Prob lem Revise Goals

Objectives

Redefine Models

Continue W ith Restoration

MONITORING

Figure 3. CALFED schematic of adaptive management.

Roles and responsibilities of the Parties pertaining to the AMP portion of the Restoration Project are listed in detail. The Licensee has agreed to a number of physical and operational changes and additions to FERC Project No. 1121 and has agreed to assume 90 percent of the initially forecast costs associated with the loss of power generation as well as other future costs.

These include, but are not limited to, cost overruns for which the Licensee is responsible, future authorized facilities modifications or increased instream flows in the event the WAF and AMF are depleted, internal costs associated with providing expertise in the AMP process, and the loss

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 x of power associated with meeting instream flow releases and Ramping Rate requirements. Upon completion of facility start-up and testing, Licensee is responsible for the operation, maintenance, replacement, and successful operation of all physical modifications to its facilities under the MOU. Licensee is also responsible for all facility and other monitoring required by the FERC license amendment for FERC Project No. 1121. NOAA Fisheries responsibilities are those it determines consistent with its mandate under the ESA. NOAA Fisheries also has the responsibility of defining recovery goals for salmon species listed under the ESA. Together the USFWS and CDFG agree to support the prescribed instream flows and Ramping Rates described in the MOU, or agreed upon through the Adaptive Management in the next relicensing proceeding for FERC Project No. 1121. USFWS and CDFG are also jointly responsible for conducting or funding a variety of monitoring, data collection and assessment, and report preparations associated with various fish population objectives. In addition, all Parties will be responsible for providing at least one representative to the AMPT and the AMTT and assuming all responsibilities and costs associated with these positions. All Parties will be individually responsible for any costs associated with their involvement in any FERC dispute resolution proceedings.

Sources of funding for the implementation of the AMP identified to date are the CALFED Monitoring Fund, the WAF, the AMF, and the Licensee. The CALFED Monitoring Fund of $1,000,000 is intended for monitoring costs associated with the Restoration Project. The WAF is a federal fund of $3,000,000 administered by the Resource Agencies per AMP protocols and intended for the sole purpose of acquiring additional instream flow releases in Battle Creek recommended under the AMP for a ten year period following the initial prescribed instream flow releases. The AMF of $3,000,000 is for the purpose of funding possible future changes to the Restoration Project developed under the AMP. The AMF is to be limited to actions under the Restoration Project directly associated with FERC Project No. 1121, and is expressly not available for funding of monitoring or construction cost overruns. In the event of the exhaustion or termination of the WAF, the AMF may be used to secure additional instream flow releases developed under the AMP. In the event of exhaustion of the WAF and AMF, the Licensee has committed up to a total of $6,000,000 for all Adaptive Management actions for Authorized Modifications to project facilities or flow operations which are determined to be necessary under Adaptive Management.

The AMP closely follows Contemporary theoretical and practical standards of adaptive management. Adaptive Management used in this plan includes elements of and, therefore, is a form of “active” adaptive management. However, because specific experimentation of instream flows and facilities modifications were not initially designed into the implementation of the AMP, the AMPT characterizes the restoration of Battle Creek as Passive Adaptive Management where changes in management are made in response to monitoring results.

The AMP bridges the theoretical and practical aspects of adaptive management by building a logical span between scientific knowledge and uncertainties, on the theoretical side, to monitoring activity schedules and budgets at the purely practical end. In between is a strong infrastructure of conceptual models and Adaptive Management Objectives.

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 xi

The reader interested in skimming the essence of this AMP, that is to quickly view the bridge between adaptive management theory and practice as applied in Battle Creek, may wish to skip to the following AMP features:

• Conceptual Models (Conceptual Models 1, 2, and 3) page 8

• Uncertainties Table (Table 3) page 12

• Adaptive Management Objectives (Section III.A) page 41

• Monitoring Activities (schedule and budget) (Table 24) page 84

The Adaptive Management objectives outlined in the AMP focus on management of hydroelectric operations within the Restoration Project to facilitate habitat changes beneficial to salmon and steelhead. There is expected to be a corresponding increase in salmon and steelhead populations as a result of these management actions. Measuring such increases is practical for larger populations such as steelhead and fall-run Chinook salmon, but proving statistically significant responses to fish populations currently at extremely low levels, such as winter-run Chinook, may not be possible. Therefore, trigger events leading to Adaptive Management actions will not be based solely on populations data, but will also rely on measurements indicating habitat conditions. The AMP objectives do not include or exclude existing or potential future propagation or supplementation activities, nor do they include specific “active” experimentation of proposed instream flows or experimental changes to hydroelectric project facilities to elucidate relationships between management actions and ecological processes, nor do they address the possibility of future development within Battle Creek.

Although many anticipated limiting factors as well as many unanticipated circumstances have been outlined in the AMP, the plan acknowledges that not all events are predictable and, invariably, surprising circumstances will arise. However, it is the nature of Adaptive Management to design studies and management programs to adapt to unforeseen circumstances.

Also, many unanticipated factors may be outside the scope of the Restoration Project. Just how an AMP responds to new circumstances is governed by a stepwise scientific process beginning with hypothesis testing of objectives through monitoring and data assessment. A timeline identifies the duration and order of monitoring activities and includes trigger events indicating that an Adaptive Management response is necessary. Adaptive Management responses would be evaluated to determine if the objective is being met and current actions should continue or if new actions are needed to meet the objectives. Adaptive Management responses could include any major or minor changes to the hydroelectric facility or the natural features of the Restoration Project. Responses to a trigger event will have limits identified by the FERC license amendment. Adaptive Management responses falling outside of those allowed by the FERC license amendment provisions would need to be addressed through established FERC processes.

Key to the Adaptive Management process is a reporting regime consistent with the ability to design and evaluate responses to Adaptive Management actions.

The AMP objectives for the restoration of salmon and steelhead focus on improvements in population dynamics, improvements to the habitat, and improvements designed to ensure safe passage of adults and juveniles. The population objectives are (1) ensure successful salmon and

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 xii steelhead spawning and juvenile production, (2) restore and recover the assemblage of anadromous salmonids (i.e., winter-run Chinook, spring-run Chinook, steelhead) that inhabit the stream’s cooler reaches during the dry season, (3) restore and recover the assemblage of anadromous salmonids (i.e., fall-run Chinook, late fall-run Chinook) that enter the stream as adults in the wet season and spawn upon arrival, and (4) ensure salmon and steelhead fully utilize available habitat in a manner that benefits all life stages, thereby maximizing natural production and full utilization of the ecosystem carrying capacity. Objectives focusing on improving the habitat of salmon and steelhead are (1) maximize habitat quantity through changes in instream flow, (2) maximize habitat quantity by ensuring safe water temperatures, (3) minimize false attraction and harmful fluctuation in thermal and flow regimes resulting from planned outages or detectable leaks from the hydroelectric project, and (4) minimize the stranding and isolation of salmon and steelhead resulting from variations in flow regimes caused by hydroelectric project operations. Objectives for the safe and reliable passage of salmon and steelhead are (1) provide upstream passage of adults at dams, (2) provide downstream passage of juveniles at dams, and (3) provide upstream passage of adults to their appropriate habitat over natural obstacles while ensuring appropriate levels of spatial separation between runs.

To determine if the population objectives of the AMP are being met, assessments of population size, trends in productivity, population substructure, and population diversity must be compared to corresponding guidelines set forth by NOAA Fisheries. The AMP has adopted NOAA Fisheries definitions of “viable populations” as the intermediate population goal and identifies the maximization of salmon and steelhead production and full utilization of carrying capacity as the final goal. The fish passage objectives are intended to assist in restoring natural process of dispersal and the habitat objectives will work to restore natural ecological variation associated with the natural function of the ecosystem. Further threats to population diversity not covered by the AMP objectives will be addressed through the AMP “linkages.”

The AMP is just one aspect of the Restoration Project and is closely linked with the other elements of the Restoration Project. Other programs within the Restoration Project cover some aspects of restoration not covered in the AMP such as facility operations and maintenance. The AMP is also linked to non-project restoration programs affecting salmon and steelhead populations both within and outside the Battle Creek watershed.

The implementation of the AMP is governed by a set of protocols. Adaptive Management activities on private land will be conducted in a manner that respects landowners’ rights and privacy and that minimizes disturbances and risks to private lands. Protocols governing data management are consistent with guidelines established by Comprehensive Monitoring, Assessment, and Research Program (CMARP) and the Environmental Protection Agency (EPA). Data and information will be made available to the public by dissemination to the appropriate agency information storage systems and an information system operated and maintained by the BCWC.

Meetings of the AMTT will be scheduled four times per year including an annual meeting in March, when possible Adaptive Management actions will be considered. The AMPT will meet at least annually in late March. These March meetings of the AMTT and AMPT are scheduled to finalize annual reports in time for funding agency deadlines. Ad hoc meetings may be scheduled by the AMTT or AMPT to address emergencies without advanced public notice, Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 xiii but such meetings will only consider the emergency at hand. All meetings will be open to the public, and all scheduled meetings will be announced to the public. Protocols also specify meeting announcement requirements, voting rules, report writing, Adaptive Management responses, proposal ranking, modification of Adaptive Management objectives, and dispute resolution.

Several Focused Studies were developed to address uncertainties and learning opportunities that may not be directly addressed by Adaptive Management objectives. These are listed in the final ten sections of the document.

Adaptive Management Plan (Reconceived) Contents

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 xiv

TABLE OF CONTENTS

ACKNOWLEDGEMENTS .........................................................................................................................................i NOTES TO THE READER....................................................................................................................................... ii PUBLIC INVOLVEMENT....................................................................................................................................... iii RESEARCH INVITATION ......................................................................................................................................iv DOCUMENT ROAD MAP........................................................................................................................................iv PREFACE ................................................................................................................................................................. vii EXECUTIVE SUMMARY ..................................................................................................................................... viii TABLE OF CONTENTS .........................................................................................................................................xiv LIST OF CONCEPTUAL MODELS ................................................................................................................... xvii LIST OF FIGURES................................................................................................................................................ xvii LIST OF TABLES.................................................................................................................................................. xvii

I. BATTLE CREEK RESTORATION PROJECT DESCRIPTION

I.A. SETTING

I.B. RESTORATION PROJECT COMPONENTS

I.B.1. Facility Modifications I.B.2. Prescribed Instream Flow Releases I.B.3. Water Acquisition Fund I.B.4. Adaptive Management Plan I.B.5. Adaptive Management Fund I.B.6. Gravel Management at Existing Dams

I.C. CONCEPTUAL MODELS

I.C.1. Watershed-Based Assessment of Limiting Factors I.C.2. Restoration Project Development Process I.C.3. Adaptive Management Development Process

I.D. KEY UNCERTAINTIES AND LEARNING OPPORTUNITIES

I.E. GOALS AND OBJECTIVES SUMMARY

I.F. DOCUMENT HISTORY AND PURPOSE

I.G. DOCUMENT ORGANIZATION

II. ADAPTIVE MANAGEMENT: DEVELOPMENT OF THIS TOOL TO ADDRESS UNCERTAINTY IN

BATTLE CREEK

II.A. DESCRIPTION OF ADAPTIVE MANAGEMENT

II.B. COMPONENTS OF ADAPTIVE MANAGEMENT

II.B.1. Step 1: Review of Available information II.B.2. Step 2: Solution Identification and Development of Conceptual Models II.B.3. Step 3: Solution Screening II.B.4. Step 4: Specification of Criteria of Success II.B.5. Step 5: Solution Implementation II.B.6. Step 6: Adaptive Responses

II.C. EXPERIMENTATION

II.C.1. Experimentation in problem definition and solution development II.C.2. Experimentation in the overall adaptive management effort II.C.3. Experimentation within component objectives

III. ADAPTIVE MANAGEMENT OF THE BATTLE CREEK RESTORATION PROJECT

III.A. ADAPTIVE MANAGEMENT OBJECTIVES

III.A.1. Objective Table Format III.A.2. Population Objectives

III.A.2.a. Population Size III.A.2.b. Trends in Productivity III.A.2.c. Population Substructure III.A.2.d. Population Diversity III.A.2.e. Viable Population Sizes and Interim Quantitative Population Goal

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 xv

III.A.2.f. Carrying Capacity III.A.3. Habitat Objectives

III.A.3.a. Habitat Quantity - Volume III.A.3.b. Water Temperature III.A.3.c. False Attraction III.A.3.d. Fish Stranding and Isolation due to Flow Fluctuations/Ramping

III.A.4. Passage Objectives III.A.4.a. Fish Ladders, Fish Screens, and Natural Barriers

III.B. ANNUAL MONITORING

III.C. FOCUSED STUDIES

III.C.1. Sediment Monitoring Plan III.C.2. Riparian III.C.3. Juvenile Habitat Use III.C.4. Cold-water Refuges III.C.5. Life History III.C.6. Fish Community Structure Evaluation

III.D. BATTLE CREEK ADAPTIVE MANAGMENT PROCESS

III.D.1. Definitions III.D.2. Structure

III.D.2.a. Adaptive Management Policy Team III.D.2.b. Adaptive Management Technical Team

III.D.3. Roles and Responsibilities III.D.3.a. Licensee III.D.3.b. NOAA Fisheries III.D.3.c. USFWS III.D.3.d. CDFG

III.D.4. Funding III.D.4.a. CALFED Monitoring Fund III.D.4.b. Water Acquisition Fund III.D.4.c. Adaptive Management Fund III.D.4.d. Licensee Commitment

III.D.5. Term III.D.5.a. Water Acquisition Fund III.D.5.b. Adaptive Management Fund III.D.5.c. FERC License

III.D.6. Adaptive Management Activities on Private Land III.D.7. Data Management III.D.8. Process

III.D.8.a. Meeting Process III.D.8.b. Reporting III.D.8.c. Adaptive Response Process III.D.8.d. Contingencies III.D.8.e. Prioritizing Response Proposals III.D.8.f. Budget Review III.D.8.g. Coleman National Fish Hatchery Adaptive Management

III.D.9. Monitoring and Data Assessment III.D.10. Funds Management III.D.11. Dispute Resolution

III.D.11.a. Disputing Party – Licensee III.D.11.b. Disputing Party – Resource Agency III.D.11.c. Water Acquisition Fund III.D.11.d. Adaptive Management Fund

III.E. LINKAGES WITH OTHER PROGRAMS

III.E.1. Restoration Project Planning

III.E.1.a. Memorandum of Understanding III.E.1.b. Construction Monitoring III.E.1.c. Facilities Transfer Agreement III.E.1.d. Facilities Monitoring Plan III.E.1.e. Operations and Maintenance Plan

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III.E.1.f. Environmental Impact Statement/Environmental Impact Report III.E.1.g. Action-Specific Implementation Plan

III.E.2. Non-Project Restoration Programs in Battle Creek III.E.2.a. Conservation Easements and Conservation Water Rights III.E.2.b. U.S. Forest Service III.E.2.c. Proposed Comprehensive Fisheries Management Plan for the Upper Sacramento River and Tributaries III.E.2.d. Sacramento Corridor Habitat Restoration Assessment III.E.2.e. Coleman National Fish Hatchery Water-Supply Intake Modifications III.E.2.f. Proposed Coleman Powerhouse Tailrace Barrier Construction III.E.2.g. Modifications to the Coleman National Fish Hatchery Barrier Weir and Associated Fish Ladders III.E.2.h. Coleman National Fish Hatchery Biological Assessment and Associated Biological Opinion III.E.2.i. Coleman National Fish Hatchery Adaptive Management Program

III.E.3. Regional Restoration Programs III.E.3.a. CBDA Ecosystem Restoration Program III.E.3.b. Central Valley Project Improvement Act III.E.3.c. Recovery Plans for Threatened or Endangered Salmonids III.E.3.d. Central Valley Salmon and Steelhead Restoration and Enhancement Plan III.E.3.e. Upper Sacramento River Fisheries and Riparian Habitat Management Plan III.E.3.f. Restoring Central Valley Streams - A Plan for Action III.E.3.g. Steelhead Restoration and Management Plan for California III.E.3.h. Delta and Sacramento River Operations and Monitoring III.E.3.i. Reference Watersheds III.E.3.j. Sport and Commercial Fisheries Management

III.E.4. Battle Creek Watershed Conservancy III.E.4.a. Potential Local Community Participation III.E.4.b. Suggested Monitoring Tasks

IV. LITERATURE CITED

V. APPENDIX OF PROPOSED FERC LICENSE ARTICLES AFFECTED BY ADAPTIVE

MANAGEMENT

VI. FOCUSED STUDY: SEDIMENT MONITORING PLAN

VII. FOCUSED STUDY: RIPARIAN HABITAT MONITORING

VIII. FOCUSED STUDY: JUVENILE SALMONID HABITAT USE STUDY

IX. FOCUSED STUDY: FISH USE OF COLD-WATER REFUGES

X. FOCUSED STUDY: BATTLE CREEK SALMONID LIFE HISTORY

X.A. BACKGROUND

X.B. BATTLE CREEK SETTING

X.C. STUDY APPROACH

X.C.1. Collect tissue samples for juvenile salmonids for genetic analysis and length at date evaluation X.C.2. Collect juvenile salmonids near spawning areas X.C.3. Distinguishing Runs of Chinook at Adult Life Stage X.C.4. Total Cost X.C.5. Possible Adaptive Responses X.C.6. References

XI. FOCUSED STUDY: FISH COMMUNITY STRUCTURE EVALUATION

XII. DIAGNOSTIC STUDY: FISH LADDER AND NATURAL BARRIER ASSESSMENT USING

RADIOTELEMETRY

XIII. APPENDIX: Summation of Calfed Bay-Delta Program Ecosystem Restoration Program

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LIST OF CONCEPTUAL MODELS

Conceptual Model 1. Battle Creek limiting factors model with key uncertainties and key linkages Conceptual Model 2. Model illustrating the development of the Restoration Project including key passive adaptive management steps Conceptual Model 3. Restoration Project Implementation Model

LIST OF FIGURES

Figure 1. CALFED schematic of adaptive management. ............................................................................................ix Figure 2. Institutional and funding relationships described in the Battle Creek Adaptive Management Plan with related watershed restoration programs and community involvement...................................................................v Figure 3. Schematic of the relationship of the Adaptive Management Plan and Adaptive Management objectives with other Restoration Project and non-project restoration activities in Battle Creek. .........................................vi Figure 4. Location Map: Battle Creek Salmon and Steelhead Restoration Project ..................................................xix Figure 5. Flow chart depicting components of all adaptive management objectives and the general relationships between the various components Figure 6. Population growth uncertainties model Figure 7. Habitat Quantity/Instream Flow Adaptive Management Model Figure 8. Water Temperature Adaptive Management Model Figure 9. False Attraction Adaptive Management Model Figure 10. Ramping rate adaptive management model Figure 11. Fish Passage Adaptive Management Model

LIST OF TABLES

Table 1. A list of acronyms used within this report. .................................................................................................... ii Table 2. Components of the Battle Creek Salmon and Steelhead Restoration Project Table 3. Uncertainties inherent in the adaptive management of Battle Creek Salmon and Steelhead Restoration

Project Table 4. The six steps of passive adaptive management identified by the CALFED Independent Science Board Table 5. Adaptive Management objectives of the Battle Creek Salmon and Steelhead Restoration Project Table 6. NOAA Fisheries viable population size guidelines. 23 Table 7. NOAA Fisheries trends and productivity guidelines. 23 Table 8. NOAA Fisheries spatial structure guidelines. 23 Table 9. NOAA Fisheries diversity guidelines. 23 Table 10. Recommended effective population sizes Table 11. Predicted population sizes of Chinook salmon and steelhead in Battle Creek after implementing restoration measures outlined in USFWS (1995) Table 12. Population Objective 1 – Spawning and juvenile production Table 13. Population Objective 2 – recover winter-run, spring-run, and steelhead Table 14. Population Objective 3 – recover fall-run and late fall-run Table 15. Population Objective 4 – carrying capacity Table 16. Habitat Objective 1 – habitat quantity/instream flow Table 17. Habitat Objective 2 – water temperature Table 18. Habitat Objective 3 – false attraction Table 19. Habitat Objective 4 – Stranding, isolation, ramping rates and flow fluctuations Table 20. Passage Objective 1 – fish ladders Table 21. Passage Objective 2—fish screens Table 22. Passage Objective 3 – natural barriers Table 23. Annual monitoring and Focused Studies as organized by objective Table 24. Linkages between the Adaptive Management of the Battle Creek Restoration Project and other planning or restoration programs and directives Table 25. CBDA Ecosystem Restoration Program visions for ecosystem elements and how the Restoration Project and Adaptive Management Plan achieves these visions

Adaptive Management Plan (Reconceived) Location Map

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Figure 4. Location Map: Battle Creek Salmon and Steelhead Restoration Project

Adaptive Management Plan (Reconceived) Battle Creek Restoration Project Description

Prepared by Terraqua, Inc. for the Adaptive Management Policy Team April 7, 2004 1

I. BATTLE CREEK RESTORATION PROJECT DESCRIPTION

I.A. Setting

Battle Creek is a tributary of the Sacramento River located in Tehama and Shasta Counties. This cold, spring-fed stream has exceptionally high flows during the dry season, making it important habitat for anadromous fish. Battle Creek may be the only remaining stream other than the main stem of the Sacramento River that can successfully sustain breeding populations of steelhead and all four runs of Chinook salmon. Battle Creek is also unique and biologically important because its numerous cold-water springs provides habitat opportunities during drought years for winter-run Chinook salmon.1

Pacific Gas and Electric Company (PG&E) owns and operates several hydroelectric power diversion facilities on the North and South Forks of Battle Creek, including Coleman Division Dam, Inskip Diversion Dam, South Diversion Dam, Wildcat Diversion Dam, Eagle Canyon Diversion Dam, and North Battle Creek Feeder Diversion Dam, and dams on Ripley Creek, Soap Creek, and Baldwin Creek. PG&E controls the majority of the flows in the anadromous fish reaches of the Battle Creek watershed.2

Salmonid populations, in general, can be affected by a recurring suite of limiting factors.

In Battle Creek, many of these typical problems are unlikely to occur due to particular watershed features, including:

• No surface water diversion occur in the forks or mainstem of Battle Creek within the project area (i.e. between Coleman Powerhouse and the upstream limits of anadromy) other than the hydroelectric project; this limits the number of dams and diversions that need to be considered.

• The existing hydro system has negligible effect on high-flow events and the wet season hydrograph due to the absence of reservoirs with significant storage capacity. This limits the projects effects on channel maintenance and stability, flushing flows and smolt out migration.

• High volume, cold (52°F) springs in both forks of the creek can be redirected to adjacent stream reaches to form cold-water refuges. Battle Creek is the most spring dominated watershed within the remaining anadromous habitat of Central Valley.

• Existing hydro system dams do not significantly alter sediment routing through the system at high flows. The dams are low (10 to 28 ft. in height) narrow structures full of sediment leaving them with little or no trap efficiency. In addition, the dams all include large sluice gates 10 to 25 sq. ft. operated several times a year during high flow to pass any accumulated sediment in the vicinity of the gates.

1 MOU 1.1

2 MOU 1.2

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• Land use dominated by large ranches (average parcel size is 400 acres in anadromous zone) that isolate the creek from development and public access disturbances.

Conservation easements are being established throughout the watershed to further buffer the stream.

• Topography in anadromous habitat, especially steep inner canyons, virtually isolate the stream from typical threats like cattle grazing, roads, and near stream logging.

• Geology/soil types of the anadromous zone and much of the rest of the watershed is resistant to surface erosion and mass-wasting,

• Within the watershed there are key activities under the control of other entities that are closely linked to the Restoration Project; specifically the operation of the Coleman National Fish Hatchery (CNFH) which is being addressed by the California Bay-Delta Authority (CBDA) Science Program workshop and reconsultation under Endangered Species Act (ESA) when the Restoration Project is complete. The potential role of the CNFH is also addressed in the current Winter-run Recovery Plan (1997). The Greater Battle Creek Watershed Working Group provides an open forum for coordinating adaptive management activities among various entities.

Several of the problems which typically affect salmonid populations are believed to occur in Battle Creek due to particular watershed features, including:

• Inadequate instream flow during the base flow period when approximately 97 percent of the unimpaired runoff is diverted out of the stream channel into adjacent canals.

(See attached water budget from Thomas R. Payne Associates (TRPA) Battle Creek Hydrology Study)

• Passage problems due to low flow over natural obstacles in the stream channel and inadequate ladders on dams. Ladders fail current standards of conveying 10 percent of the stream flow by one order of magnitude. In addition, ladders are vulnerable to failure from debris (especially Alaska Steep pass units) and they are all situated on dams where they cannot be cleared of debris during wet season.

• Temperature problems for cold-water fish species result from diversion of cold-water springs on both forks directly into canals and away from adjacent stream channels. In addition, lower flows resulting from hydropower diversions increase the heat gain as the water travels down the canyon.

• Entrainment resulting from no fish screens and extremely high percentage of flow diverted (up to 97 percent of base flow).

• Powerhouse operations disrupt stream function and stability by: 1) causing rapid flow fluctuations of up to 200 cfs which can lead to redd-dewatering, and stranding and isolation of juvenile fish, 2) causing rapid changes in water temperature regime, and

2) diverting as much as 97 percent of the water from the North Fork into the South Fork leading to potential false attraction of returning adults to non-natal habitat that is at risk of rapid, detrimental fluctuations in water temperature.

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I.B. Restoration Project Components3

The proposed Battle Creek Salmon and Steelhead Restoration Project includes the following elements (see Table 2 for a summary):

I.B.1. Facility Modifications3

A. Coleman Diversion Dam:

• Install a tailrace connector from Inskip Powerhouse to Coleman Canal and a water bypass facility around Inskip Powerhouse to Coleman Canal. The Inskip Powerhouse bypass facility will be the most economical alternative that still provides the functional equivalent of the existing Inskip Powerhouse bypass system and will deliver that system’s design flow of water to the Coleman Canal.

• Decommission the dam and appurtenant facilities.

B. Inskip Diversion Dam:

• Install a National Marine Fisheries Service (NOAA Fisheries)/California Department of Fish and Game (CDFG) approved Fail-Safe Fish Screen.

• Install a NOAA Fisheries/CDFG approved Fail-Safe Fish Ladder.

• Install a tailrace connector from South Powerhouse to Inskip Canal concurrent with, or prior to, the Inskip Diversion Dam fish screen.

C. South Diversion Dam:

• Decommission the dam, related water conveyance and appurtenant facilities.

D.…