Fish Restoration Program Agreement Implementation Strategy Habitat Restoration and Other Actions for Listed Delta Fish Department of Water Resources and Department of Fish and Game in coordination with the US Fish and Wildlife Service and the National Marine Fisheries Service Cover: Prospect Island, Sacramento River Deep Water Ship Channel, and Liberty Island (Photo Credit: Dale Kolke) State of California The Resources Agency Department of Water Resources March 2012 Fish Restoration Program Agreement Implementation Strategy Habitat Restoration and Other Actions for Listed Delta Fish Prepared by: With assistance from: Heidi Rooks Department of Fish and Game Stephani Spaar Dave Zezulak Dennis McEwan Fred Jurick Jason Roberts Laura Flournoy Carl Wilcox Tim Smith Jim Starr Gina Benigno Gina Van Klompenburg Pamela Lindholm Tim Stevens Ling Chu Chandra Ferrari Laurence Kerckhoff Delta Stewardship Council Kristal Davis‐Fadtke PAGE INTENTIONALLY LEFT BLANK ii Table of Contents 1. Introduction ........................................................................................................................ 1 1.1 Purpose ................................................................................................................................. 1 1.2 FRPA Goals and Objectives ................................................................................................... 2 1.3 Program Description ............................................................................................................. 2 1.3.1 Program Structure and Support ..................................................................................... 3 1.3.2 Estimated Costs, Acreage Targets, and Timeline ........................................................... 5 1.4 FRPA’s Relationship to Other Programs ............................................................................... 7 2. Proposed Restoration Actions.............................................................................................. 9 2.1 Restoration Scientific Principles ........................................................................................... 9 2.2. Action Components ........................................................................................................... 10 2.2.1 Financing ...................................................................................................................... 10 2.2.2 Restoration Action Identification and Land Acquisition .............................................. 11 2.2.3 Legal and Land Management Issues ............................................................................ 12 2.2.4 Stakeholder Involvement and Public Outreach ........................................................... 13 2.2.5 Planning and Design ..................................................................................................... 13 2.2.6 Environmental Compliance and Permits ..................................................................... 13 2.2.7 Monitoring and Adaptive Management ...................................................................... 14 2.2.8 Construction ................................................................................................................. 14 2.2.9 Post‐Project Management ........................................................................................... 15 2.3. Near Term Actions ............................................................................................................. 15 2.4 Potential Future Actions ..................................................................................................... 17 2.5 Restoration Challenges ....................................................................................................... 22 3. Action Selection Framework ............................................................................................. 23 3.1 Action Identification Process .............................................................................................. 24 3.2 Action Selection Criteria ..................................................................................................... 24 3.3 Action Acreage Crediting Evaluation .................................................................................. 26 3.4 Review of Action Progress .................................................................................................. 26 4.0 Monitoring and Reporting ............................................................................................... 27 4.1 Required Monitoring Under the Biological Opinions and ITP ............................................ 27 4.2 Monitoring Plan Implementation ....................................................................................... 28 iii 4.3 Reporting Requirements ..................................................................................................... 29 4.4 Adaptive Management ....................................................................................................... 32 5.0 Post‐Project Maintenance ............................................................................................... 33 5.1 Property Transfer and Management Costs......................................................................... 34 5.2 Funding ............................................................................................................................... 34 6.0 References ....................................................................................................................... 34 Appendix A. Fish Restoration Program Agreement Appendix B. Required Actions of the Fish Restoration Program Agreement Appendix C. BDCP Habitat Credit Memorandum of Agreement Appendix D. WREM 65 and SWPAO Project Charter Appendix E. Permits Likely to be Required for Near Term Actions Appendix F. Descriptions of Near Term Actions Appendix G. Annual Report Template Appendix H. Conflict Resolution Form iv List of Figures and Tables Figure 1: Roles, responsibilities, and coordination of the FRPA program……………………………………4 Figure 2: Near‐term habitat restoration actions in the Cache Slough Complex…………………………16 Figure 3: Near‐term habitat restoration actions in Suisun Marsh……………………………………………..18 Figure 4: Near‐term habitat restoration actions in the Yolo Bypass………………………………………….19 Figure 5: Land elevations within the Northern Delta………………………………………………………………..21 Figure 6: Framework for analyzing and selecting proposed actions for implementation………….25 Table 1: Estimated costs and acreage targets for potential FRPA restoration actions………………..6 Table 2: Potential metrics to be evaluated……………….………………………………………………………………30 v PAGE INTENTIONALLY LEFT BLANK vi 1. Introduction 1.1 Purpose The Fish Restoration Program Agreement (FRPA) (Appendix A), between the Department of Fish and Game (DFG) and the Department of Water Resources (DWR), was signed on October 18, 2010. FRPA addresses specific habitat restoration requirements of the US Fish and Wildlife Service (USFWS) and National Marine Fisheries Service S)(NMF biological opinions (Biological Opinions) for State Water Project (SWP) and Central Valley Project (CVP) operations. FRPA is also intended to address the habitat requirements of the DFG Longfin Smelt Incidental Take Permit (ITP) for SWP Delta operations. The primary objective of the FRPA program is to implement the fish habitat restoration requirements and related actions of the Biological Opinions and the ITP in the Delta, Suisun Marsh, and Yolo Bypass and is focused on 8,000 acres of intertidal and associated subtidal habitat to benefit delta smelt, including 800 acres of mesohaline habitat to benefit longfin smelt, and a number of related actions for salmonids. DFG and DWR intend that habitat restoration actions implemented in compliance with the USFWS biological opinion that also meet the habitat restoration requirements of the ITP will operate to satisfy the acreage requirements of the ITP. The purpose of this Implementation Strategy is to describe the process by which DWR and DFG will implement the FRPA program, and to satisfy Section B of FRPA. Section B of FRPA requires DWR, with assistance from DFG, to develop an Implementation Schedule that will identify restoration actions, estimated costs, targeted acreage, and a timeline for DWR’s implementation of restoration actions to satisfy DWR’s obligations under the Biological Opinions and ITP. Appendix B lists the specific habitat restoration requirements of FRPA, the Biological Opinions, and the ITP that pertain to this program. This document lays out the strategy to address these requirements. In addition, DWR and DFG will complete the necessary environmental compliance documents to implement site specific habitat restoration projects; this may include tiering from existing programmatic documents where appropriate. Pursuant to FRPA, DFG will work cooperatively with and assist DWR in establishing the management and financial framework necessary to implement the FRPA program. DWR, with assistance from DFG, will begin a process to fund, plan, and implement actions, including aquatic habitat restoration to benefit delta smelt, longfin smelt, and winter‐run and spring‐run Chinook salmon (hereafter referred to as Covered Fish Species) to mitigate impacts to these species caused by the SWP Delta operations. Specifically, these actions include: • Delta Smelt Biological Opinion Reasonable and Prudent Alternative (RPA) Component 4; 1 • NMFS Biological Opinion RPA Actions 1.2.6 and 1.6.2 in