Attachment_1-Coleman_NFH_Adaptive_Management_Plan.pdf

Coleman National Fish Hatchery Adaptive Management Plan

November 2016

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Coleman National Fish Hatchery Adaptive Management Plan

Final Report November 1, 2016

Prepared for:

U.S. Department of the Interior, Bureau of Reclamation

Prepared by:

Cramer Fish Sciences under Contract No. R12PX20045 ii

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Acknowledgments Numerous individuals contributed to the development of this document. In particular, we acknowledge members of the Technical Advisory Committee commissioned to provide advice and guidance throughout the course of this project: Naseem Alston (NMFS), Matt Brown (USFWS), Amanda Cranford (NMFS), Laurie Earley (USFWS), Gene Geary (PG&E), Scott Hamelberg (USFWS), Doug Killam (CDFW), Mary Marshall (Reclamation), Kevin Niemela (USFWS), Robert Null (USFWS), Trang Nguyen (Reclamation), Jason Roberts (CDFW), Steve Tussing (BCWC), and Jonathan Walsh (PG&E). Their patience and expertise is gratefully acknowledged. An independent science review panel provided critical comments, which helped to improve this document. Several members of the public provided constructive comments and useful information, which also helped to improve this document.

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Public Involvement An open and inclusive process was used to develop the Coleman National Fish Hatchery Adaptive Management Plan. Two public meetings were held, one early on to aid in scoping the plan, and a second meeting during the public comment period for the draft plan. Public comments and responses to those comments are separately available in a comment log.

Members of the public are encouraged to stay engaged as this adaptive management plan is implemented by attending the Greater Battle Creek Watershed Working Group (GBCWWG) meetings. More information about the group is available at http://www.battle-creek.net/, or by writing the Battle Creek Watershed Conservancy, P.O. Box 606, Manton, CA 96059.

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Executive Summary The Battle Creek watershed, like many in the west, is a complex environment, providing important opportunities for both the natural and man-made environments. Agency and stakeholder representatives with interests in the Battle Creek watershed have worked over the last two decades to reconcile the conflicts between ecological functions and human services.

These efforts have mainly focused on conserving and restoring aquatic habitats for native salmonid reproduction and growth, while preserving the use of water resources for hydropower production and water diversions. Mandated fish hatchery operations at the Coleman National Fish Hatchery (CNFH) is another longstanding use that increases the complexity of these reconciliation efforts.

Restoration of the upper Battle Creek watershed, motivated through FERC relicensing of PG&E hydropower facilities, focuses on providing fish access to historical habitat for the re-establishment of naturally occurring salmonid populations. The Battle Creek watershed is considered a highly important watershed that historically supported large numbers and a broad diversity of anadromous salmonids. Infrastructure modifications associated with the Battle Creek Salmon and Steelhead Restoration Project (BCRP) began in early 2010. The goal of the BCRP is to provide high quality habitat and improve fish passage throughout 48 miles of stream habitat. Once completed, the BCRP will be adaptively managed as described in a project-specific adaptive management plan (BCRP-AMP).

The CNFH is located on the north bank of Battle Creek, approximately three miles east of the Sacramento River. The hatchery barrier weir and fish ladder system is the first substantial man-made structure immigrating anadromous fish encounter when returning to Battle Creek. The CNFH is unique among hatcheries in California, in that it is not located immediately downstream from the reservoir dam it is intended to mitigate. Since its establishment in 1942, the CNFH has served as an important mitigation component of the Federal Central Valley Project (CVP), partially compensating for lost natural salmonid production resulting from construction of Shasta and Keswick dams. The hatchery is considered a positive contributor to regional socioeconomics.

To provide for better hatchery operations and outcomes, and to partially mitigate for potential impacts to restoration efforts in the watershed, substantial modifications to the CNFH have occurred over the last decade to address long-standing concerns about: (1) the hatchery’s potential to amplify the transmission of fish diseases; (2) adult fish passage through the hatchery’s barrier weir and fish ladder system; and (3) entrainment of natural origin juvenile salmonids emigrating from upper Battle Creek. However concerns remain about the continuing impacts the CNFH may have on the timely restoration of impaired salmonid populations in the upper Battle Creek watershed. In 2004 an independent technical panel examined the compatibility of CNFH operations and restoration of salmonid populations in Battle Creek. This panel recommended development of an adaptive management for the CNFH. This document describes a plan that supports adaptive management of the CNFH, and to the extent possible, integrated adaptive management of the CNFH and BCRP. The overall aim is to maximize compatibility of the CNFH with the BCRP, thereby contributing to the further reconciliation of ecological functions and human services in the Battle Creek watershed.

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Coleman National Fish Hatchery Adaptive Management Plan

Adaptive management provides a rational approach for addressing issues where competing but uncertain solutions exist, and for which management cannot be delayed until the issues and solutions are fully understood. It is often considered for use in ecological systems where:

1. Conflicts exist

2. The stakes are high

3. There is uncertainty about the best way to proceed

Adaptive management is an iterative process that allows for the formal analysis of data and information as a means of framing new choices, providing understanding, and making decisions.

The adaptive management cycle used in development of the CNFH-AMP closely follows the cycle developed through the CALFED Ecosystem Restoration Program, which is the cycle used in the BCRP-AMP (Figure ES.1).

Figure ES.1. Diagram of the adaptive management cycle developed for the CNFH-AMP.

(Adapted from Healey et al. 2008). The route with thicker arrows generally follows the passive adaptive management cycle used in the BCRP-AMP. The shaded area (upper right) indicates where active adaptive management can occur within the cycle.

To develop the CNFH-AMP, a Technical Advisory Committee (TAC) comprising the major agency, restoration, and utility stakeholders in the Battle Creek watershed, was consulted on every major element of the AMP. TAC guidance included the following:

• Establish the purpose, goal, and objectives.

• Comment on plan development and organization.

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• Define the Issue/Problem statements.

• Provide data (and identify data gaps), and more importantly assess the quality of the data available for analysis.

• Provide technical colleague review of two quantitative life-cycle models, developed to support issue analysis.

• Provide advice on conceptual life cycle models for the fish species in question.

• Identify a governance structure to coordinate the implementation of the CNFH-AMP with restoration efforts in the BCRP-AMP.

The TAC also identified three critical principals that would guide CNFH-AMP development and implementation:

• The CNFH will continue to operate to partially mitigate for the loss of anadromous salmonid production associated with the construction of Shasta Dam.

• The CNFH-AMP assumes restoration of the Battle Creek watershed will occur as described.

• Implementation of the CNFH-AMP will be closely coordinated with BCRP-AMP implementation, but the two projects will remain separate efforts that operate under different authorities.

The CNFH-AMP provides a structure to support future operations of the CNFH in a watershed that has undergone substantial restoration. To the extent possible, the document provides for the coordinated implementation of the CNFH and the BCRP under an integrated adaptive management framework. In order to increase the plan’s ease of use and utility, the main document provides focused information about the need for adaptive management, issue identification and evaluation, and key factors affecting implementation (i.e., funding sources, governance, and decision making). Documents providing relevant technical details and directly supporting information are included as appendixes:

• Description of the CNFH, its setting and information about the scope of this project

• Description of a coordinated governance structure for the CNFH and BCRP adaptive management plans

• Conceptual models and detailed analyses of identified issues

• Documentation for the Chinook and steelhead life cycle models

• An integrated monitoring plan x xi

Table of Contents Acknowledgments.......................................................................................................................... iii

Public Involvement ..........................................................................................................................v

Executive Summary ...................................................................................................................... vii

Coleman National Fish Hatchery Adaptive Management Plan ............................................... viii

Table of Contents ........................................................................................................................... xi

List of Figures .............................................................................................................................. xiii

List of Tables .................................................................................................................................xv List of Appendixes ...................................................................................................................... xvii

List of Acronyms ......................................................................................................................... xix

Chapter 1: Introduction

1.1 Coleman National Fish Hatchery Adaptive Management Plan Purpose Goal and Objectives

1.2 Plan Development and Organization

1.2.1 Document Organization

1.3 Literature Cited

Chapter 2: Framework and Processes for Adaptive Management of the Coleman National Fish Hatchery

2.1 Adaptive Management Cycle

2.2 Governance and decision-making

2.3 Tools and processes to optimize CNFH-AMP Implementation

2.3.1 Future issue identification and assessment

2.3.2 Tools and Processes for assessment evaluation and adaptation

2.4 Funding for Implementation of the Coleman National Fish Hatchery Adaptive Management Plan

2.5 Literature Cited

Chapter 3: Issue Identification and Evaluation

3.1 Issue Statements

3.1.1 CNFH Issues Statements

3.1.2 BCRP Issues Statements

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3.2 Summary of Issue Statement Evaluations

3.3 Literature Cited

Chapter 4: Issue Synthesis and Action Evaluation

4.1 Issue Synthesis

4.2 Tier I Action Identification and Routing

4.3 Making Adjustments: Completing the Adaptive Management Cycle

4.4 Tier 2 Actions

4.4 Literature Cited

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List of Figures Figure ES.1. Diagram illustrating steps in the CNFH and BCRP adaptive management cycle related to action selection, implementation, and evaluation of performance.

Figure 1.1. Schematic diagram of the Battle Creek watershed identifying the modifications to hydropower infrastructure that will be completed through the course of the restoration project.

Figure 1.2. Location of Coleman National Fish Hatchery and other notable features of the Sacramento River system between Shasta Dam and Red Bluff Diversion Dam.

Figure 2.1. Diagram of the adaptive management cycle developed for use in the CALFED Ecosystem Restoration Program and used in the BCRP-AMP.

Figure 2.2. Diagram of the adaptive management cycle developed for the CNFH-AMP.

Figure 2.3. Diagram of the proposed decision-making structure to support coordinated implementation of the CNFH-AMP and BCRP-AMP.

Figure 4.1. Diagram illustrating steps in the CNFH and BCRP adaptive management cycle related to action selection, implementation, and evaluation of performance.

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List of Tables Table 1.1. Purpose, goals, and objectives of the BCRP-AMP, CNFH, and the CNFH-AMP.

Table 1.2. Members of the CNFH-AMP Technical Advisory Committee.

Table 2.1. Fiscal year 2012 allocations of Reclamation funding provided to support the USFWS programs at CNFH and LSNFH and associated field facilities.

Table 3.1. Steelhead - Overall summary for levels of importance and understanding estimated from the analysis of CNFH and BCRP issues that potentially affect natural-origin steelhead in Battle Creek.

Table 3.2. Spring Chinook - Overall summary for levels of importance and understanding estimated from the analysis of CNFH and BCRP program issues that potentially affect natural-origin spring Chinook salmon in Battle Creek.

Table 3.3. Fall Chinook - Overall summary for levels of importance and understanding estimated from the analysis of CNFH and BCRP program issues that potentially affect natural-origin fall Chinook salmon in Battle Creek.

Table 3.4. Late-fall Chinook - Overall summary for levels of importance and understanding estimated from the analysis of CNFH and BCRP program issues that potentially affect natural-origin late-fall Chinook salmon in Battle Creek.

Table 3.5. Winter Chinook - Overall summary for levels of importance and understanding estimated from the analysis of CNFH and BCRP program issues that potentially affect natural-origin winter Chinook salmon in Battle Creek.

Table 4.1. Summary of issues determinations and resulting evaluation standards and related actions.

Table 4.2. Null hypothesis, approach, and result actions for Tier 1 diagnostic studies.

Table 4.3. Performance measures, monitoring and data assessment, success standards, contingencies, and resources required for Tier 1 implementation actions.

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List of Appendixes Appendix A: Coleman National Fish Hatchery Setting and Description

Appendix B: Memorandum of Understanding Regarding Integrated Adaptive Management of the Battle Creek Salmon and Steelhead Restoration Project and Coleman National Fish Hatchery

Appendix C: Conceptual Models and Issue Analysis

Appendix D: A Life-cycle Model for Chinook Salmon in Battle Creek, CA

Appendix E: A Life-cycle Model for Partially Anadromous Rainbow Trout in Battle Creek, CA

Appendix F: Integrated Monitoring Plan xviii xix

List of Acronyms ACL........................................Annual Catch Limit

AFRP......................................Anadromous Fish Restoration Program

AMPT ....................................Adaptive Management Policy Team

AMTT ....................................Adaptive Management Technical Team

BA ..........................................Biological Assessment

BCRP .....................................Battle Creek Salmon and Steelhead Restoration Project

BCRP-AMP ...........................Battle Creek Salmon and Steelhead Restoration Project Adaptive Management Plan

BCWC ....................................Battle Creek Watershed Conservancy

BKD .......................................Bacterial Kidney Disease

CDFG .....................................California Department of Fish and Game

CDFW ....................................California Department of Fish and Wildlife

CFM .......................................Constant Fractional Marking

CFS ........................................Cubic Feet per Second

CNFH .....................................Coleman National Fish Hatchery

CNFH-AMP ...........................Coleman National Fish Hatchery Adaptive Management Plan

CNFH-AMP TAC ..................Coleman National Fish Hatchery Adaptive Management Plan Technical Advisory Committee

CVI .........................................Central Valley Index

CVPIA....................................Central Valley Project Improvement Act

CVRWQCB ...........................Central Valley Regional Water Quality Control Board

CWT .......................................Coded Wire Tag

ERM .......................................Enteric Red Mouth

ESA ........................................Endangered Species Act

ESU ........................................Evolutionary Significant Unit

FGC ........................................Fish and Game Commission

FMWT....................................Fall Mid-water Trawl

FPP .........................................Fish per Pound

GPM .......................................Gallons per Minute

GBCWWG .............................Greater Battle Creek Watershed Working Group

HMT .......................................Hatchery Management Team xx

IHNV......................................Infectious Hematopoietic Necrosis Virus

IPNV ......................................Infectious Pancreatic Necrosis Virus

IS ............................................Issue Statements

LCM .......................................Life Cycle Model

LSNFH ...................................Livingston Stone National Fish Hatchery

MOU ......................................Memorandum of Understanding

NMFS .....................................National Marine Fisheries Service

OFL ........................................Overfishing Limit

OSP ........................................Ocean Salmon Project

PBT ........................................Parental Based Tagging

PFMC .....................................Pacific Fisheries Management Council

PG&E .....................................Pacific Gas and Electric Company pHOS......................................Proportion of Hatchery Origin Spawners

PNI .........................................Proportionate Natural Influence

PSMFC ...................................Pacific States Marine Fisheries Commission

RMPC ....................................Regional Mark Processing Center

RST ........................................Rotary Screw Trap

SAR ........................................Smolt-to-Adult Return

SDFPF ....................................Skinner Delta Fish Protective Facility

SI ............................................Sacramento Index

SRFC ......................................Sacramento River Fall Chinook

TAC........................................Technical Advisory Committee

USFWS ..................................United State Fish and Wildlife Service

VIE .........................................Visible Implant Elastomer

VSP ........................................Viable Salmonid Population

WD .........................................Whirling Disease

Chapter 1: Introduction Agency and stakeholder representatives with interests in the Battle Creek watershed have worked over the last two decades to reconcile the conflicts between ecological functions and human services. Reconciliation efforts have mainly focused on conserving and restoring aquatic habitats for native salmonid reproduction and growth, while preserving the use of water resources for hydropower production and water diversions. Mandated fish hatchery operations is another longstanding use that adds to the complexity of these reconciliation efforts. Formal protection of three salmonids stocks under the California and Federal endangered species acts (ESA), and the subsequent identification of the Battle Creek watershed as important recovery habitat (NMFS 2014), provided further motivation to improve ecological functions, while striving to optimize existing human services.

A major outcome of the reconciliation efforts is substantial restoration of the upper Battle Creek watershed, which focuses on providing naturally occurring salmonids access to historical habitat.

The Battle Creek watershed is considered a highly important and unique watershed that historically supported large numbers and a broad diversity of anadromous salmonids (Jones and Stokes 2005a, Terraqua 2004). The watershed is part of the Basalt and Porous Lava diversity group, one of four geographic regions in the Central valley considered important to the formulation of Evolutionary Significant Units (ESU) for Chinook salmon and Central Valley steelhead (NMFS 2014). The majority of habitat for this diversity group occurs above Shasta Dam; thus, the Battle Creek watershed is considered highly important in the context of endangered and threatened species recovery planning for winter and spring Chinook salmon, and Central Valley steelhead (NMFS 2014).

Although highly unique and historically important to several salmonids stocks, the Battle Creek watershed has been substantially modified to support hydropower production (Jones and Stokes 2005a). Initiated in early 2000, the Battle Creek Salmon and Steelhead Restoration Project (BCRP) focuses on restoring in-stream flows and improving fish passage through modification of existing hydropower infrastructure (Figure 1.1). The goal is to provide high quality habitat and improve fish passage throughout 48 miles of stream habitat, which together support self-sustaining populations of several Chinook salmon stocks, and Central Valley steelhead (Terraqua 2004). Once completed, the BCRP will be adaptively managed as described in a project-specific adaptive management plan (Terraqua 2004).

Figure 1.1. Schematic diagram of the Battle Creek watershed identifying the modifications to hydropower infrastructure to be completed through the course of the restoration project. See Jones and Stokes (2005a) for more details on the restoration project.

Since its establishment in 1942, the Coleman National Fish Hatchery (CNFH) has served as an important mitigation component of the Federal Central Valley Project (CVP), partially compensating for lost natural salmonid production resulting from construction of Shasta and Keswick dams (Richardson 1987). The hatchery is considered highly successful, and is a positive contributor to regional socioeconomics (USFWS 2011). Yet the physical infrastructure and operations of the CNFH have the potential to adversely affect the attainment of BCRP goals and objectives.

The CNFH is located on the north bank of Battle Creek, approximately three miles east of the Sacramento River (Figure 1.2). The CNFH is unique among anadromous salmonid mitigation hatcheries in California, in that it is not located immediately downstream from the reservoir dam it is intended to mitigate.

Figure 1.2. Location of Coleman National Fish Hatchery and other notable features of the Sacramento River system between Shasta Dam and Red Bluff Diversion Dam (Figure from

USFWS 2011).

Substantial modifications to the CNFH have occurred over the last decade to address what many considered the major adverse impacts of the hatchery on the watershed and its living resources.

These modifications addressed long-standing concerns about: (1) the hatchery’s potential to amplify the transmission of fish diseases; (2) adult fish passage through the hatchery’s barrier weir and fish ladder system; and (3) entrainment of natural origin juvenile salmonids emigrating from upper Battle Creek (USFWS 2011). Yet concerns remain about the continuing impacts the CNFH may have on the timely restoration of impaired salmonid populations in the upper Battle Creek watershed. In 2004 an independent technical panel examined the compatibility of CNFH operations and restoration of salmonid populations in Battle Creek (Technical Review Panel 2004). A major conclusion of this panel stated, The success of the Battle Creek restoration project will depend a great deal on CNFH and possibly Livingston Stone National Hatchery operations. Project planners and USFWS staff need to develop a detailed plan to ensure that hatchery operations are compatible with the recovery goals for Battle Creek.

The expectation is that development of an adaptive management plan for the CNFH will provide:

(1) objective assessment of the importance and understanding of currently identified hatchery issues that may adversely affect the restoration of salmonid populations in upper Battle Creek;

and (2) decision support processes to identify, evaluate, and address existing and future concerns.

The adaptive management plan developed to guide ongoing management of the BCRP (Terraqua 2004) does not include the CNFH because the two programs operate under different authorities and responsibilities (Jones and Stokes 2005a). Thus, this document describes a plan that supports adaptive management of the CNFH, and to the extent possible, integrated adaptive management of the CNFH and BCRP. The overall aim is to maximize compatibility of the CNFH with the BCRP, thereby contributing to the further reconciliation of ecological functions and human services in the Battle Creek watershed.

1.1 Coleman National Fish Hatchery Adaptive Management Plan

Purpose Goal and Objectives

Clear statements of the purpose, goal, and objectives are foundational elements of any adaptive management plan. The purpose describes what the plan is intended to do, while the goal and objectives describe what the plan is expected to achieve. A technical advisory committee (TAC or CNFH-AMP TAC; see Section 1.2 below) was closely consulted during development of the purpose, goal, and objectives for the Coleman National Fish Hatchery Adaptive Management Plan (CNFH-AMP). Key parameters and several important assumptions that directly influence the stated purpose, goal, and objectives also were identified during TAC consultation:

• The CNFH will continue to operate to partially mitigate for the loss of anadromous salmonid production associated with the construction of Shasta Dam (Jones and Stokes 2005a). Thus, the CNFH-AMP goal assumes the continued coexistence of the CNFH and the BCRP.

• The CNFH-AMP assumes restoration of the Battle Creek watershed will occur as described in Jones and Stokes (2005a), and implementation of the Battle Creek Salmon and Steelhead Restoration Project Adaptive Management Plan (BCRP-AMP) will occur as described in Terraqua (2004).

• The CNFH-AMP will be closely coordinated with the BCRP-AMP. Together the two adaptive management plans will form a single integrated framework for adaptive management in Battle Creek. However, the goals and objectives of the BCRP-AMP are not the same as the goal and objectives of the CNFH-AMP (Table 1.1). To maximize the chances of successful outcomes from the integrated adaptive management framework, it is assumed that the goal for the CNFH-AMP will seek to achieve compatibility with the BCRP by acknowledging that adjustment and adaptations can occur in: (1) CNFH programs and operations; (2) the BCRP (including Pacific Gas and Electric Company (PG&E) facilities within the Federal Energy Regulatory Commission’s Battle Creek Hydroelectric Project boundaries); or (3) areas of overlapping interest, such as lower Battle Creek.

• The goal and objectives of the CNFH-AMP are not the same as the goal and objectives of the CNFH (Table 1.1). It is assumed that responsibilities described in the 1993 agreement between USFWS and Reclamation will continue. Specifically, the agreement stipulates that USFWS will continue to operate, maintain, and evaluate the facility for the salvage, protection, and preservation of fish spawned in the upper Sacramento River Basin prior to the construction of Shasta and Keswick dams. Reclamation will assume financial responsibility for the facility and arrange for recovery costs from project beneficiaries in accordance with Federal reclamation law (Jones and Stokes 2005a).

Establishing a goal and objectives for the CNFH-AMP that differ from the goal and objectives established for the hatchery creates a circumstance requiring special treatment in the application of adaptive management. This is discussed further in Chapter 2.

The purpose of the CNFH-AMP is to acknowledge, identify, study, and evaluate uncertainties regarding the operation of a large scale fish hatchery in a watershed being restored for natural salmonid populations. The CNFH-AMP is intended to closely coordinate with the BCRP-AMP, so that together the two adaptive management plans form a single integrated framework for adaptive management in Battle Creek.

The goal of the CNFH-AMP is to provide solutions and processes to support optimization of CNFH programs, operations, and infrastructure so that the hatchery mitigation goals and objectives are achieved, while maximizing its compatibility with the BCRP.

The objectives of the CNFH-AMP are as follows:

• Describe and evaluate ten issues related to the CNFH identified by the TAC, and identify solutions to those issues considered of most importance. Develop cost and resource estimates to implement the Tier 1 (i.e., top priority) solutions by 2021.

• Describe and evaluate four key issues of direct relevance to Battle Creek restoration, and determine their importance in achieving BCRP goals.

• Provide an integrated monitoring plan and quantitative life-cycle models to support the coordinated assessment of the CNFH and BCRP.

• Identify and describe diagnostic studies that address the greatest areas of uncertainty related to the CNFH. Provide cost and resource estimates to complete the Tier 1 diagnostic studies by 2021.

• Describe a governance structure that provides for ongoing communication and coordinated decision-making between the CNFH and BCRP projects throughout their implementation.

• Describe the steps and processes for adaptive management in sufficient detail so that the CNFH-AMP remains a durable plan with ongoing utility.

These objectives are structured to support the aim of having two adaptive management plans that form a single integrated framework for adaptive management in Battle Creek.

Table 1.1. Purpose, goals, and objectives of the BCRP-AMP (from Terraqua 2004), CNFH (from USFWS 2011), and the CNFH-AMP.

BCRP-AMP CNFH CNFH-AMP

Purpose

Restore anadromous fish habitat in Battle Creek and its tributaries while minimizing the loss of clean and renewable energy produced by the Hydroelectric Project.

The CNFH provides partial mitigation for the loss of fish habitat due to the construction of Shasta and Keswick dams.

The CNFH-AMP will acknowledge, identify, study, and evaluate uncertainties regarding the operation of a large scale fish hatchery in a watershed being restored for natural salmonid populations.

Goals

Restore and enhance approximately 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 (FERC Project No. 1121). The additional 48 miles of anadromous fish habitat is being restored to support an assemblage of fish species including four separate runs (races) of Chinook salmon and steelhead. Winter-run Chinook, spring-run Chinook, and steelhead have been identified as the priority species for recovery because they are listed under the state or federal ESA.

Fall & Late-fall Chinook salmon

Contribute to ocean harvest.

Contribute to the commercial fishery, ocean sport fishery, and freshwater sport fishery.

Provide adequate escapement to the hatchery for broodstock.

Minimizing negative impacts to natural populations.

Provide fish for future recovery efforts, if needed.

Steelhead

Mitigate for fishery losses resulting from the construction of Shasta and Keswick dams.

Contribute to the sport fishery in the Sacramento River and Delta.

Provide adequate broodstock to the hatchery.

Minimize risks to natural populations.

The goal of the CNFH-AMP is to provide solutions and processes to support optimization of CNFH programs, operations, and infrastructure so that the hatchery mitigation goals and objectives are achieved, while maximizing its compatibility with the BCRP.

Objectives

Restoration of self-sustaining populations of four races of Chinook salmon and steelhead, and their habitats in the Battle Creek watershed through a voluntary partnership with state and federal agencies, a third party donor(s), and PG&E.

Natural spawner escapement objectives/1:

Winter-run = 2,500

CNFH objectives are to attain the following numerical targets/2

Fall Chinook:

Number of broodstock = 5,200 Annual juvenile release = 12,000,000 (@ 90 fish/pound (fish/lb))

Late-fall Chinook:

Number of broodstock = 540 Annual juvenile release = 1,000,000 (@ 13 fish/lb)

Describe and evaluate ten issues related to the CNFH identified by the TAC, and identify solutions to those issues considered of most importance. Develop cost and resource estimates to implement the Tier 1 (i.e., top priority) solutions by 2021.

Describe and evaluate four key issues of direct relevance to Battle Creek restoration and determine their importance in achieving BCRP goals.

BCRP-AMP CNFH CNFH-AMP

Spring-run = 2,500

Fall-run = 4,500

Late-fall run = 4,500

Steelhead = 5,700

Steelhead:

Number of broodstock = 400 Annual juvenile release = 600,000 (@ 4 fish/lb)

Up-front certainty regarding specific restoration components, including Resource Agency prescribed in-stream flow releases, selected decommissioning of dams at key locations in the watershed, dedication of water diversion rights for instream purposes at decommissioned sites, construction of tailrace connectors, and installation of fish ladders and fail-safe fish screens.

Provide an integrated monitoring plan and quantitative life-cycle models to support the coordinated assessment of the CNFH and BCRP.

Timely implementation and completion of restoration activities.

Identify and describe diagnostic studies that address the greatest areas of uncertainty. Provide cost and resource estimates to complete the Tier 1 diagnostic studies by 2021.

Joint development and implementation of a long-term adaptive management plan with dedicated funding sources to ensure the continued success of restoration efforts under this partnership.

Describe a governance structure that provides for ongoing communication and coordinated decision-making between the CNFH and BCRP projects throughout their implementation.

Describe the steps and processes for adaptive management in sufficient detail so that the CNFH-AMP remains a durable plan with ongoing utility.

/1. Escapement numbers are predicted population sizes following restoration based on USFWS (1995) as cited in Terraqua (2004).

/2. The number of broodstock listed for fall and late-fall Chinook and steelhead is the minimum number of adult fish needed to meet the production target. However, in practice the CNFH will increase the number of broodstock to increase the representation of individuals throughout the run and maintain genetic variability. The increased numbers are approximately 8,000 for fall Chinook; 1,000 late-fall Chinook; and 800 steelhead.

1.2 Plan Development and Organization

An open and inclusive process was used to develop the CNFH-AMP. The consultant team engaged and received input from the TAC throughout plan conception, development, and revision (Table 1.2). Many parts of the plan are a result of TAC discussions and input. Two public meetings were held, one early on to aid in scoping the plan, and a second meeting during the public comment period for the draft plan. An independent science panel was commissioned to evaluate the technical merits of the draft plan. The science panel was provided with a specific review charge, and its comments were used to revise the plan. Finally, Federal and State agency review occurred to maximize the veracity and utility of the plan to those agencies with direct involvement in the BCRP and the CNFH.

Table 1.2. Members and affiliation of the CNFH-AMP Technical Advisory Committee (TAC).

Technical Advisory Committee Members Affiliation Naseem Alston NOAA, National Marine Fisheries Service

Mike Berry CA Department of Fish and Wildlife

Matt Brown U.S. Fish & Wildlife Service

Amanda Cranford NOAA, National Marine Fisheries Service

Laurie Earley U.S. Fish & Wildlife Service

Brett Galyean U.S. Fish & Wildlife Service

Gene Geary Pacific Gas & Electric Company

Scott Hamelberg U.S. Fish & Wildlife Service

Doug Killam CA Department of Fish & Wildlife

Mary Marshall U.S. Bureau of Reclamation

Kevin Niemela U.S. Fish & Wildlife Service

Robert Null U.S. Fish & Wildlife Service

Trang Nguyen U.S. Bureau of Reclamation

Jason Roberts CA Department of Fish and Wildlife

Steve Tussing Battle Creek Watershed Conservancy

Jonathan Walsh Pacific Gas & Electric Company

1.2.1 Document Organization

This document provides an adaptive management plan to support future operations of the CNFH in a watershed that has undergone substantial restoration. To the extent possible, the document provides for the coordinated implementation of the CNFH and the BCRP under an integrated adaptive management framework. In order to increase the plan’s ease of use and utility, the main document provides focused information, while documents providing relevant technical details and directly supporting information are included as appendixes. This adaptive management plan is based on the CNFH facilities and operations as described in the 2011 biological assessment for the hatchery (USFWS 2011). Appendix A provides a description of the CNFH, its setting, and information about the scope of this project.

Adaptive management is defined in this document as a set of tools and processes that can provide information to learn about the system, and if needed, change the system (Hollings 1978). The CNFH-AMP relies on an adaptive management cycle developed for use in the CALFED Ecosystem Restoration Program (see CALFED 2000, and Healey et al. 2008 for more details).

This same adaptive management cycle is used in the BCRP-AMP, and thus serves as a central component of the integrated framework under which both plans will be implemented. The adaptive management cycle and its component steps are described in Chapter 2.

A functional governance structure is essential to successful implementation of an adaptive management plan. Appendix B provides a detailed description of the coordinated governance structure that will be used to support information communication and assessment, conflict resolution, and decision-making throughout implementation of the CNFH and BCRP adaptive management plans.

The issues that have the potential to adversely affect the CNFH’s compatibility with the BCRP, and a summary of their evaluations are presented in Chapter 3. Summary evaluations of four key BCRP issues also are presented in Chapter 3. All of these issues were evaluated in the context of four conceptual models. These conceptual models along with detailed analyses of the issues are presented in Appendix C. Two quantitative life-cycle models were developed to estimate the effects many of the identified issues may have on Chinook salmon and Central Valley steelhead populations in Battle Creek. Documentation for these models is presented in Appendixes D and E.

Chapter 4 provides details on the identification and prioritization of actions or studies to address issues determined to be of importance, or with incomplete understanding. Further, an integrated monitoring plan is provided (Appendix F) to guide the coordinated collection and analysis of data used to assess both the CNFH and the BCRP, based on pre-determined performance measures. This plan also identifies monitoring efforts to inform long-term status and trends metrics for target fish stocks, as well as the data collection efforts to support the quantitative life-cycle models.

A wealth of information is available on the Battle Creek watershed, the CNFH, and the BCRP (see for example, the Battle Creek Watershed Conservancy web site (http://www.battle-creek.net) or Jones and Stokes 2005a). However, this document is not intended to provide an extensive review of this information. Salient facts and information are included where appropriate, with references to source materials that provide detailed information.

1.3 Literature Cited

CALFED. 2000. Ecosystem Restoration Program Plan: Strategic Plan for Ecosystem Restoration. Technical appendix in: CALFED Bay-Delta Program Final EIS/EIR.

Healey, M.C., M.D. Dettinger, and R.B. Norgaard, eds. 2008. The State of Bay-Delta Science, 2008. Sacramento,CA: CALFED Science Program. 174 pp.

Hollings, C.S. 1978. Adaptive environmental assessment and management. New York: Wiley Publisher. 377 p.

Jones and Stokes. 2005a. Battle Creek salmon and steelhead restoration project final environmental impact statement/environmental impact report. Volume I, Report. Sacramento, CA.

NMFS (National Marine Fisheries Service). 2014. Final Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter run Chinook Salmon and Central Valley Spring run Chinook Salmon and the Distinct Population Segment of Central Valley Steelhead.

Sacramento Protected Resources Division, CA. 273p.

Richardson, T.H. 1987. An analysis of the effectiveness of the mitigation plan for Shasta and Keswick dams. U.S. Department of Interior, Fish and Wildlife Service, Division of Ecological Services. Sacramento, CA. 84 p.

Technical Review Panel. 2004. CALFED Bay-Delta Program, Report of the Technical Review Panel - Compatibility of Coleman National Fish Hatchery Operations and Restoration of Anadromous Salmonids in Battle Creek. 68 p.

Terraqua. 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, and California Department of Fish and Game. Wauconda, Washington. 238 p.

USFWS (United States Fish and Wildlife Service). 2011. Biological assessment of artificial propagation at Coleman National Fish Hatchery and Livingston Stone National Fish Hatchery:

program description and incidental take of Chinook salmon and steelhead. U.S. Fish and Wildlife Service, Red Bluff and Coleman National Fish Hatchery Complex, CA. 406 p.

Chapter 2: Framework and Processes for Adaptive Management of the Coleman National Fish Hatchery

We do not learn from a system that is constant. This is not serious if the system is known, is static, and presents no surprises. But resource systems are exactly the opposite. They are known only very partially, which will always be so; they are dynamic and they produce endless surprises –from the collapse of fisheries to the reemergence of other ecosystems. And the act of management and harvesting changes the fundamental structure of the resource itself. Walters (1986).

A variety of processes and techniques have been advanced to guide those who seek to plan and implement a project or program through adaptive management (see Stankey et al. 2005 for a thoughtful review). At the project level, an adaptive management framework typically involves a cyclical process that makes explicit linkages among the steps of issue identification, information acquisition, management decisions, and management action. Adaptive management provides a rational approach for addressing issues where competing but uncertain solutions exist, and for which management cannot be delayed until the issues and solutions are fully understood (Walters 1986). It is often considered for use in ecological systems where:

1. Conflicts exist. The overarching issue for the CNFH-AMP concerns the potential conflicts between the existence of the hatchery, and the effects its ongoing operations may have on the timely restoration of anadromous salmonid populations in Battle Creek.

2. The stakes are high. The CNFH provides partial mitigation for impacts associated with Shasta Dam, which created the largest reservoir in California’s Central Valley. The completion of Shasta dam is estimated to have blocked “approximately 50% of the Chinook salmon spawning beds in the Sacramento River system” (Skinner 1958). The CNFH is considered highly successful, contributing substantially to the multi-million dollar ocean and in-land fisheries, and it has become an important part of the local community (USFWS 2011). Yet Battle Creek is a unique watershed that is considered highly important in the context of endangered and threatened species recovery planning for winter and spring Chinook salmon, and Central Valley steelhead (NMFS 2014).

Approximately $150 million will be spent to restore the upper Battle Creek watershed, with the expectation that the restored area will support self-sustaining populations of threatened and endangered anadromous salmonids (Jones and Stokes 2005a, Terraqua 2004).

3. There is uncertainty about the best way to proceed. A fundamental premise of adaptive management is that knowledge of ecological systems is not only incomplete but elusive (Walters and Holling 1990). The CNFH-AMP TAC identified ten issues associated with the hatchery and its operations that may adversely impact the BCRP. Further, four key issues related to the BCRP were identified, and their impacts also were evaluated.

However, uncertainties exist regarding the importance and understanding of these issues, as well as the most appropriate course of action to address each issue. Thus, the purpose of the CNFH-AMP is to acknowledge, identify, study, and evaluate uncertainties regarding the operation of a large-scale fish hatchery in a watershed being restored for natural salmonid populations.

2.1 Adaptive Management Cycle

The adaptive management cycle used in this plan is based on the approach developed for the CALFED Ecosystem Restoration Program (Figure 2.1). This adaptive management cycle also is used in the BCRP-AMP (Terraqua 2004).

Figure 2.1. Diagram of the adaptive management cycle developed for use in the CALFED Ecosystem Restoration Program, and used in the BCRP-AMP (from Healey 2001, as cited in Terraqua 2004).

The BCRP-AMP identified six steps of passive adaptive management in its processes to identify and evaluate problems, and to develop solutions:

1. Review the available information so as to define the problem as precisely as possible.

2. Think of plausible solutions to the management problem. Describe these solutions in terms of conceptual models of system behavior, and its response to possible management interventions.

3. Subject these solutions to some form of structured analysis to determine which solution offers the greatest promise of success.

4. Specify criteria (indicators or measures) of success or failure of the most promising solution.

5. Implement the most promising solution, and monitor the system response according to the criteria developed in step 4.

6. Adjust the design of the solution from time to time according to the results of monitoring in an attempt to make it work better.

The CNFH-AMP employs an adaptive management cycle similar to that used in the BCRP-AMP (Figure 2.2), although some important changes were incorporated to more accurately reflect the order of the steps and process used to develop the CNFH-AMP, and to address the unique relationship among the CNFH, the BCRP-AMP, and this adaptive management plan.

Figure 2.2. Diagram of the adaptive management cycle developed for the CNFH-AMP.

(Adapted from Healey et al. 2008). The route with thicker arrows generally follows the passive adaptive management cycle used in the BCRP-AMP. The shaded area (upper right) indicates where active adaptive management can occur within the cycle.

The CNFH-AMP adaptive management cycle generally relies on a passive adaptive management approach. In passive adaptive management historical information is used to frame a single best approach along a linear path assumed to be correct (i.e., it is based on the belief that past assumptions and antecedent conditions still apply; Stankey et al. 2005). This approach applies a formal, rigorous, albeit retrospective analysis to data and information as a means of framing new choices, providing understanding, and making decisions. The routes in the CNFH-AMP adaptive management cycle involving diagnostic studies and their input into other steps in the cycle is considered the active adaptive management loop (Figure 2.2). Active adaptive management allows for the purposeful integration of experimentation into policy and management design and implementation (Kusel et al. 1996 as cited in Stankey et al. 2005).

However, the application of active adaptive management in the CNFH-AMP focuses on the use of experimentation to reduce uncertainty associated with defining/clarifying issues, evaluating issue importance, and evaluating alternative solutions.

The following steps were completed to develop the CNFH-AMP using the adaptive management cycle shown in Figure 2.2. Long-term implementation of the CNFH-AMP will require revisiting each of the steps in this adaptive management cycle, and critically evaluate the outputs from each step based on incorporation of new data and information.

1. Establish goals and objectives. Goals and objectives for the CNFH-AMP were developed in collaboration with the TAC. As noted in Chapter 1, the CNFH-AMP goal and objectives are not the same as the goal and objectives for the hatchery or the BCRP-AMP (see Table 1.1). Solutions selected to address important issues are intended to maximize the compatibility of the CNFH and its operations with the BCRP; however, overall assessment of CNFH-AMP performance will be based on how well the plan achieves its unique goal and objectives, not the goal and objectives of the CNFH or the BCRP. This is an unusual situation. It is more common for a project’s adaptive management plan to have the same goals and objectives as the project (e.g., as was done for the BCRP-AMP).

Further, it is more common for two projects that co-occur in the same watershed, and with interest in the same species, to establish shared goals and objectives. However, this was not possible in this case due to the differing authorities and responsibilities underlying the two projects (Appendix B).

Establishing separate goals and objectives for the project and its adaptive management plan has both pros and cons. Separate goals and objectives provide greater flexibility to those implementing the CNFH-AMP in responding to changing…