Water Operations in the Central Valley, California

The West Coast Region’s California Central Valley Office conducts Endangered Species Act (ESA) Section 7 consultations in the Sacramento-San Joaquin Delta, and oversees the operations of the State Water Project (SWP) and Central Valley Project (CVP), which includes 5 reservoirs and 2 major water pumping plants in California’s Central Valley.

Long-Term Operations of the Central Valley Project and State Water Project

In 2009, NOAA Fisheries issued a biological opinion to the U.S. Bureau of Reclamation (Reclamation) which concluded that the long-term operations of the CVP and SWP (including reservoir management and pumping operations) in California’s Central Valley were likely to jeopardize the continued existence of Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, California Central Valley steelhead, the southern distinct population segment of North American green sturgeon, and Southern Resident killer whales (which depend on Chinook salmon for food).

On April 7, 2011, NOAA Fisheries provided an RPA amendment (PDF, 189 pages), which, consistent with the Delta Stewardship Council’s Independent Review Panel, corrected errors in the 2009 RPA and provided clarification. 

On August 2, 2016, Reclamation, the federal action agency, and the California Department of Water Resources, the applicant, jointly requested the reinitiation of Endangered Species Act (ESA) consultation on the coordinated long-term operation of the CVP and SWP (PDF, 2 pages). NOAA Fisheries accepted the reinitiation request on August 17, 2016 (PDF, 2 pages).

On January 31, 2019, Reclamation transmitted their Biological Assessment and Cover letter (PDF, 2 pages) to NOAA Fisheries (PDF, 247 pages). As stated in the Biological Assessment, the purpose of this action is “…to continue the coordinated long-term operation of the CVP and SWP to maximize water supply delivery and optimize power generation consistent with applicable laws, contractual obligations, and agreements; and to increase operational flexibility by focusing on nonoperational measures to avoid significant adverse effects.”

2019 Biological Opinion

NOAA Fisheries finalized and issued its biological opinion on the coordinated operations of the CVP and SWP on October 21, 2019. NOAA Fisheries carefully evaluated the impacts of CVP and SWP water operations on ESA-listed species, including Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon, California Central Valley steelhead,southern distinct population segment of North American green sturgeon, and Southern Resident killer whales. The proposal included habitat management measures in the Delta and entrainment management related to water exports in the South Delta.

NOAA Fisheries documented impacts from the proposed operations and worked with Reclamation to modify their proposed action to minimize and offset those impacts. NOAA Fisheries undertook two independent scientific peer reviews and utilized the best science available in the development of its biological opinion. Ultimately, NOAA Fisheries concluded that Reclamation’s proposed operations will not jeopardize threatened or endangered species or adversely modify their designated critical habitats.

View the 2019 biological opinion

Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat

NOAA Fisheries completed a Magnuson-Stevens Fishery Conservation and Management Act (MSA) Essential Fish Habitat (EFH) Consultation for the Long Term Operations of the CVP and SWP (PDF, 45 pages) on January 24, 2020. The EFH Consultation includes discretionary Conservation Recommendations to conserve the EFH of these species. The EFH Conservation Recommendations address effects to Pacific Coast Salmon, Pacific coast groundfish and coastal pelagic species.

Along the West Coast, the Pacific Fishery Management Council identifies habitats that fall within “Habitat Areas of Particular Concern” (HAPC) and recommends these to NOAA Fisheries consistent with the MSA. HAPCs are considered high priority areas for conservation, management, or research because they are important to ecosystem function, sensitive to human activities, stressed by development, or are rare. These areas provide important ecological functions and/or are especially vulnerable to degradation and can be designated based on either specific habitat types or discrete areas. HAPCs are a discrete subset of EFH. This EFH consultation focuses on addressing any adverse effects the proposed action may incur in the following designated HAPCs:

• HAPCs for Chinook salmon are: complex channel and floodplain habitat, spawning habitat, thermal refugia, estuaries, and submerged aquatic vegetation as described in Appendix A to the Pacific Coast Salmon Fishery Management Plan (PDF, 227 pages).
• HAPCs for Pacific coast groundfish are: estuaries, rocky reefs, canopy-forming kelp, seagrasses, and “areas of interest” as described in Amendment 19 to the Pacific coast groundfish Fishery Management Plan. Species likely to occur in the action area include starry flounder and English sole.
• EFH for coastal pelagic species is described in Amendment 8 to the Coastal Pelagic Species Fishery Management Plan and explains the habitat requirements of five pelagic species. Species most likely to occur in the action area include Northern anchovy and Pacific sardine.

Related Documents:

• Proposed 2017 RPA Amendment:
  • Reclamation's detailed comments (March 22, 2017)
  • Reclamation's response (January 25, 2017)
  • NOAA Fisheries Draft Proposed 2017 RPA Amendment (January 19, 2017)
  • NOAA Fisheries response to Reclamation's request for Shasta RPA adjustments (August 17, 2016)
  • Bureau of Reclamation's request for Shasta RPA adjustments (August 2, 2016)
• Actions associated with implementation of the 2009 Biological Opinion for CVP and SWP Operations
• Documents for U.S. Fish and Wildlife Service Biological Opinion

Technical Working Groups

• Salmon Monitoring Team (SaMT), previously Delta Operations for Salmonids and Sturgeon (DOSS)
• Stanislaus Operations Group (SOG)
• Sacramento River Temperature Task Group (SRTTG)
• Stanislaus Nonnative Predator Research Program

Delta Consultations

We conduct ESA section 7 consultations with Federal action agencies that authorize, fund, or carry out projects in the Sacramento-San Joaquin Delta, including construction (e.g., residential boat docks, marinas, agricultural structures including intakes and seasonal earthen barriers to maintain pump efficiency), dredging for the maintenance of two major ports (Stockton and Sacramento) and their associated deep water shipping channels in the Sacramento and San Joaquin rivers, large and small scale habitat restoration projects, research, and aquatic weed management and non-native invasive species control.

Restoration

NOAA Fisheries is involved in numerous habitat restoration projects. In the Sacramento Valley, the Yolo Bypass is a major flood bypass located in Yolo and Solano counties. The Yolo Bypass diverts floodwaters from the Sacramento River away from the City of Sacramento and nearby communities through a system of weirs. Most of the land is privately owned and is used for agriculture; the rest is marshland managed by wildlife areas, providing ideal habitat for terrestrial, avian, and aquatic species, which is also utilized for fishing, hunting, and other recreational activities. NOAA Fisheries provides guidance to federal, state, and local stakeholders for listed salmonids and sturgeon that utilize the Yolo Bypass. This includes providing consultation on restoration actions (Yolo Bypass Habitat Restoration Program), multi-stakeholder partnerships, habitat conservation planning, and collaboration with NGOs to improve floodplain habitat function (Nigiri Project).

Reports

• Effects of Water Project Operations on Juvenile Salmonid Migration and Survival in the South Delta Report (January 2017)