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Ecosystem Restoration Program Conservation Strategy for Restoration of the Sacramento-San Joaquin Delta, Sacramento and San Joaq

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Ecosystem Restoration Program Conservation Strategy for Restoration of the Sacramento-San Joaquin Delta, Sacramento and San Joaq Ecosystem Restoration Program Conservation Strategy for Restoration of the Sacramento-San Joaquin Delta, Sacramento Valley and San Joaquin Valley Regions May 2014 Department of Fish and U. S. Fish and Wildlife Service NOAA Fisheries Wildlife 650 Capitol Mall, Suite 8-300 National Marine Fisheries 830 S Street Sacramento, CA 95814 Service Sacramento, CA 95811 (916) 930 - 5603 650 Capitol Mall, Suite 5-100 (916) 445-1700 Sacramento, CA 95814 (916) 930-3600 The Ecosystem Restoration Program (ERP) Implementing Agencies (California Department of Fish and Wildlife [CDFW], United States Fish and Wildlife Service [USFWS], and National Marine Fisheries Service [NMFS]) provide this Conservation Strategy (Strategy) to help guide future environmental restoration in the Sacramento- San Joaquin Delta and its watershed (Focus Area). This Strategy, built on lessons learned during Stage 1 of CALFED (2000 through 2007), was developed by CDFW collaboratively with USFWS and NMFS. The Strategy identifies ERP goals and conservation priorities and processes for Stage 2 of CALFED (2008 through 2030), while providing impetus for improvement in the future. It provides flexibility so that management decisions can be made adaptively based on new scientific findings, changing circumstances, and new or modified conservation priorities. All agencies, groups, or individuals interested in resource conservation and management within the Focus Area are encouraged to use this document to help guide and coordinate their activities. Foreword To reduce conflicts between interest groups and move towards a restored Sacramento- San Joaquin Delta (Delta) ecosystem, the CALFED Bay-Delta Program (CALFED) was established in 1994 with the signing of the Bay-Delta Accord. The original purpose of the CALFED Program was to address four interrelated objectives: Levee System Integrity, Ecosystem Restoration, Water Supply Reliability, and Water Quality. Over the next six years specific goals and objectives of the 30-year CALFED program were elucidated in the CALFED Multi-Species Conservation Strategy (MSCS), the Programmatic Environmental Impact Statement/Environmental Impact Report (EIS/EIR), and the Record of Decision (ROD) (CALFED 2000c, 2000d, 2000e). In 2009 the California legislature passed the Delta Reform Act, thereby authorizing new planning efforts to achieve the co-equal goals of water supply reliability and a healthy Delta ecosystem. This act created two new State agencies to help accomplish the co- equal goals, the Delta Stewardship Council (DSC) and the Sacramento-San Joaquin Delta Conservancy (Conservancy). As the State implementing agency for the CALFED Ecosystem Restoration Program (ERP), the California Department of Fish and Wildlife (CDFW) (previously known as the Department of Fish and Game) is pursuing a seamless transition from the previous structure, guided by the California Bay-Delta Authority and CALFED Science Program, to the new governance structure established by the Delta Reform Act. CDFW, the United States Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS) coordinate with the DSC and the Conservancy in the implementation of ERP activities, obtaining their guidance to assure consistency with the Delta Plan being developed by the DSC. Coordination with the DSC to promote consistency with the Delta Plan and other planning efforts will ensure that DSC actions are informed by future implementation of ERP and information gained from ERP's first seven years of restoration, research, monitoring, and assessment efforts. The stated mission of CALFED “…is to develop a long-term comprehensive plan that would restore ecosystem health and improve water management for beneficial uses of the Bay-Delta system.” ERP is the principal CALFED program component designed to restore the ecological health of the Bay-Delta ecosystem. The approach of ERP is to restore or mimic ecological processes and to increase and improve aquatic and terrestrial habitats to support stable, self-sustaining populations of diverse and valuable species. Implementation of the 30-Year CALFED ROD (ROD) was divided into two stages, Stage 1 (2000-2007) and Stage 2 (2008–2030). The Stage 1 Plan for Ecosystem Restoration was developed for implementation during the first seven years of the program. It was acknowledged that judging progress could not be accurately assessed during the early phases of the program. The ROD stipulated that to be successfully implemented, ERP must have a minimum of $150 million annually of dedicated funding during Stage 1 Implementation. In addition, long term implementation of ERP would include an adaptive management framework for addressing program performance. Conservation Strategy for Restoration of the i Sacramento-San Joaquin Delta, Sacramento Valley and San Joaquin Valley Regions This Conservation Strategy describes Stage 2 conservation priorities of the Sacramento-San Joaquin Delta and the Sacramento Valley and San Joaquin Valley Regions. It responds to analysis of Stage 1 research, restoration, and monitoring activities that determined the CALFED through-Delta conveyance alternative, as it had been implemented, did not achieve sufficient progress in sustaining viable populations of endangered and threatened aquatic species. Findings of Stage 1 ERP implementation are presented in this document only to the extent they inform scientific understanding of the system since the certification of the ROD in 2000. CDFW was the lead agency in developing the Conservation Strategy, in coordination with USFWS and NMFS. This final version incorporates public and agency comments. Coordination of future updates to the Conservation Strategy will be made concurrently with updates to the Delta Plan, if and when appropriate. This Conservation Strategy will be reviewed and updated, as necessary, until implementation of the ROD is completed (2030). Conservation Strategy for Restoration of the ii Sacramento-San Joaquin Delta, Sacramento Valley and San Joaquin Valley Regions TABLE OF CONTENTS Foreword .......................................................................................................................... i Introduction ..................................................................................................................... 1 Purpose and Intended Use .............................................................................................. 1 ERP Goals ...................................................................................................................... 3 Lessons Learned in Stage 1 and Management Considerations for Stage 2 .................... 5 Other Considerations for ERP ......................................................................................... 6 Integration and Relationship of the Conservation Strategy to Other Planning Efforts ..... 8 Ecological Setting and Vision for Restoration of the Delta and its Watershed ............... 12 SECTION 1: Sacramento-San Joaquin Delta Region ................................................... 15 Background ................................................................................................................... 15 I. Ecosystem Processes ........................................................................................... 16 II. Habitats ................................................................................................................. 29 III. Stressors ............................................................................................................... 43 IV. Species ................................................................................................................. 62 SECTION 2: Sacramento Valley Region ....................................................................... 85 Background ................................................................................................................... 85 I. Ecosystem Processes ........................................................................................... 86 II. Habitats ................................................................................................................. 96 III. Stressors ............................................................................................................. 100 IV. Species ............................................................................................................... 108 SECTION 3: San Joaquin Valley Region .................................................................... 119 Background ................................................................................................................. 119 I. Ecosystem Processes ......................................................................................... 121 II. Habitats ............................................................................................................... 130 III. Stressors ............................................................................................................. 134 IV. Species ............................................................................................................... 141 SECTION 4: Adaptive Management............................................................................ 154 I. A Three Phase Adaptive Management Framework ............................................. 154 II. Performance Measures ....................................................................................... 163 III. Monitoring Program ............................................................................................
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