Biological Opinion and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project

National Marine Fisheries Service (NMFS) | June 4th, 2009

The purpose of this document is to present NOAA’s National Marine Fisheries Service’s (NMFS) biological and conference opinion (Opinion), about whether the U.S. Burea

The purpose of this document is to present NOAA’s National Marine Fisheries Service’s (NMFS) biological and conference opinion (Opinion), about whether the U.S. Bureau of Reclamation’s (Reclamation) proposed long-term operations of the Central Valley Project (CVP), operated in coordination with the State Water Project (SWP; hereafter referred to as CVP/SWP operations, the proposed action, or the project), is likely to jeopardize the continued existence of the following species  Endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha, hereafter referred to as winter-run)  Threatened Central Valley spring-run Chinook salmon (O. tshawytscha, hereafter referred to as spring-run)  Threatened Central Valley (CV) steelhead (O. mykiss)  Threatened Central California Coast (CCC) steelhead (O. mykiss)  Threatened Southern Distinct Population Segment (DPS) of North American green sturgeon (Acipenser medirostris, hereafter referred to as Southern DPS of green sturgeon)  Endangered Southern Resident killer whales (Orcinus orca, hereafter referred to as Southern Residents)  or destroy or adversely modify the designated critical habitat of the above salmon and steelhead species, or proposed critical habitat for Southern DPS of green sturgeon. This Opinion is based on the best scientific and commercial information available. 

Biological opinion and conference opinion on the long-term operations of the Central Valley Project and State Water Project

National Marine Fisheries Service (NMFS) | June 4th, 2009

Biological opinion for the California Water Fix (National Marine Fisheries Service)

National Marine Fisheries Service (NMFS) | June 16th, 2017

Based on the best available scientific and commercial information, the Biological Opinion (Opinion) concludes that the Project is not likely to jeopardize the continued e

Based on the best available scientific and commercial information, the Biological Opinion (Opinion) concludes that the Project is not likely to jeopardize the continued existence of federally listed: • Endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), • Threatened Central Valley spring-run Chinook salmon (0. tshawytscha), • Threatened Central Valley steelhead ( 0. my kiss), • Threatened Southern Distinct Population Segment (DPS) of North American green sturgeon (Acipenser medirostris), and • Endangered Southern Resident killer whales ( Orcinus area). NMFS concludes that the Project is not likely to destroy or adversely modify the designated critical habitats of: • Sacramento River winter-run Chinook salmon, • Central Valley spring-run Chinook salmon, • Central Valley steelhead, and • Southern DPS of North American green sturgeon. Southern Resident killer whales critical habitat is outside of the action area. As required by section 7 of the ESA, for the above species, NMFS has included an incidental take statement for activities within the proposed Project that do not require further analysis. The incidental take statement describes reasonable and prudent measures NMFS considers necessary or appropriate to minimize the impact of incidental take associated with these activities. The take statement also sets forth nondiscretionary terms and conditions, including monitoring and reporting requirements, that the U.S. Bureau of Reclamation (Reclamation) as the Federal action agency, must comply with to carry out the reasonable and prudent measures. Incidental take from activities that meet these terms and conditions will be exempt from the ESA’s prohibition against the take of listed species. The Project for this consultation is a “mixed programmatic action” because it approves some actions that are not subject to further section 7 consultation as well as provides programmatic review of future actions that would be authorized, at a later time. For actions that are expected to be developed in the future (mitigation/restoration, monitoring, adaptive management), take of listed species would not occur until those future actions were authorized. For other actions (construction and operations), NMFS is providing an incidental take statement with this Opinion. The enclosed Opinion is based on information provided in the Reclamation’s transmittal letter and biological assessment, correspondence and discussions between NMFS, Reclamation, and California Department of Water Resources staff, and consultants; a final proposed action issued on June 2, 2017; comments received from Reclamation; peer review reports from the Delta Stewardship Council’s Delta Science Program; and an extensive literature review completed by NMFS staff. A complete administrative record of this consultation is on file at the NMFS California Central Valley Office. NMFS also concurs with Reclamation’s conclusion that the proposed action is not likely to adversely affect threatened Central California Coast steelhead (O. mykiss), endangered Central California Coast coho salmon (O. kisutch), or the designated critical habitat for Central California Coast steelhead. Designated critical habitat for Central California Coast coho salmon is not included in the action area. NMFS reviewed the likely effects of the proposed action on essential fish habitat (EFH), pursuant to section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1855(b)), and concluded that the Project would adversely affect the EFH of Pacific Coast salmon, Coastal Pelagic species, and Pacific Coast Groundfish in the action area. We have included these EFH consultation results in Section 3 of this document. The EFH consultation itself includes Conservation Recommendations specific to the adverse effects to EFH identified during our review. Reclamation has a statutory requirement under section 305(b)(4)(B) of the MSA to submit a detailed written response to NMFS within 30 days of receipt of these EFH conservation recommendations, and 10 days in advance of any final approval of the action if the response is inconsistent with any of NMFS’ EFH Conservation Recommendations. The written response must include a description of measures adopted by Reclamation for avoiding, minimizing, or mitigating the impact of the Project on EFH (50 CFR § 600.920(k)). If unable to complete a final response within 30 days, Reclamation should provide an interim written response within 30 days before submitting its final response. In the case of a response that is inconsistent with our recommendations, Reclamation must explain its reasons for not following the recommendations, including the scientific justification for any disagreements with NMFS over the anticipated effects of the Project and the measures needed to avoid, minimize, or mitigate (also referred to by NMFS as measures that "offset") such effects.

Biological Opinion for the California Water Fix (US Fish and Wildlife Service)

U.S. Fish and Wildlife Service (FWS) | June 23rd, 2017

This consultation examines whether the California WaterFix (CWF) Proposed Action (PA) is likely to jeopardize the continued existence of the threatened California red-leg

This consultation examines whether the California WaterFix (CWF) Proposed Action (PA) is likely to jeopardize the continued existence of the threatened California red-legged frog (Rana draytonii), threatened California tiger salamander (Central California Distinct Population Segment; Ambystoma californiense), threatened delta smelt (Hypomesus transpacificus), threatened giant garter snake (Thamnophis gigas\ endangered Least bell's vireo (Vireo belliipusillus), endangered San Joaquin kit fox (Vulpes macrotis mutica), threatened valley elderberry longhorn beetle (Desmocerus californicus dimorphus), threatened vernal pool fairy shrimp (Branchinecta lynchi), endangered vernal pool tadpole shrimp (Lepidurus packardi), and threatened western yellow-billed cuckoo (Coccyzus americanus occidentalis). Additionally, this consultation addresses whether the CWF PA is likely to destroy or adversely modify delta smelt critical habitat. The attached Final BiOp incorporates relevant information provided by the action agencies and applicant, including comments, changes, and additions to the CWF provided since consultation was initiated. The Service has prepared a mixed programmatic BiOp on the CWF. This BiOp represents the culmination of consultation on a mix of standard-level and programmatic-level project elements. An analysis and conclusion of whether or not the entire CWF action is likely to jeopardize each listed species or destroy or adversely modify designated critical habitat is included in this BiOp. All activities addressed programmatically will be subject to a subsequent consultation on future Federal actions in order to proceed. The following activities analyzed as a standard consultation are: (1) construction of the tunnels; (2) expansions and other modifications of Clifton Court Forebay; (3) associated infrastructure; (4) geotechnical explorations, (5) compensatory mitigation associated with construction except the North Delta Diversions (NDD), Head of Old River Gate (HORG), and Contra Costa Water District (CCWD) settlement agreement facilities; and (6) specific construction-related conservation measures including preconstruction surveys for listed terrestrial species. Where incidental take of threatened or endangered species is reasonably certain to occur, an Incidental Take Statement for these activities is included with this BiOp. The following activities requiring future Federal approvals and therefore addressed programmatically are: (1) construction of the NDD and associated structures; (2) construction of the HORG; (3) construction of the CCWD settlement agreement facilities; (4) operations of new and existing CVP and SWP water facilities under dual conveyance; (5) future maintenance; (5) future monitoring; (6) compensatory mitigation associated with construction of the NDD, HORG, and CCWD settlement agreement facilities; and (7) the CWF Adaptive Management Program. In order to ensure that future actions developed for the CWF are consistent with this analysis, Reclamation and DWR have proposed a framework consisting of Guiding Principles that are analyzed as part of this BiOp. One or more subsequent consultations will be needed to address activities associated with future approvals. No Incidental Take Statement is included for activities addressed programmatically because those subsequent consultations will address incidental take associated with those activities. The Service has analyzed the operational scenario for CWF included in the BA. The agencies recognize this operational scenario will change between now and the time that the CWF facilities are operational. Changes to the operational scenario will be analyzed in subsequent consultation. The attached BiOp addresses effects of the CWF to 16 federally-listed species and designated critical habitat. Appendix A of the BiOp includes justifications for the species and critical habitat that were determined not likely to be adversely affected. Effects to the remainder of the species and critical habitat are addressed in the BiOp. The Service has determined that the CWF is not likely to jeopardize the continued existence of any of these species, and is not likely to destroy or adversely modify designated critical habitat.

Biological Opinion on Long-term Operation of the Central Valley Project and the State Water Project

National Marine Fisheries Service (NMFS) | October 21st, 2019

Biological opinion on the coordinated operations of the Central Valley Project (CVP) and State Water Project (SWP)

U.S. Fish and Wildlife Service (FWS) | December 15th, 2008

On May 16, 2008, the U.S. Bureau of Reclamation and the California Department of Water Resources asked the Service to initiate consultation on the Long-Term Operational C

On May 16, 2008, the U.S. Bureau of Reclamation and the California Department of Water Resources asked the Service to initiate consultation on the Long-Term Operational Criteria and Plan (OCAP) for coordination of the Central Valley Project and State Water Project, specifically concerning the delta smelt and its critical habitat. (See OCAP Legal Archives.) On December 15, 2008, the Fish & Wildlife Service issued a biological opinion (BO) on the Long-Term Operational Criteria and Plan (OCAP) for coordination of the Central Valley Project and State Water Project. The Service determined that the continued operation of these two water projects, as described in the plan, was likely to jeopardize the continued existence of the delta smelt and adversely modify its critical habitat. The inclusion by the Service of reasonable and prudent alternatives, and their acceptance by the water agencies, avoided jeopardy and adverse modification.

Bisphenols in San Francisco Bay: Wastewater, Stormwater, and Margin Sediment Monitoring

San Francisco Estuary Institute (SFEI) | October 28th, 2022

Bisphenols are a class of synthetic, mobile, endocrine-disrupting chemicals. Bisphenol A (BPA), the most well-studied bisphenol, is produced and used in vast quantities w

Bisphenols are a class of synthetic, mobile, endocrine-disrupting chemicals. Bisphenol A (BPA), the most well-studied bisphenol, is produced and used in vast quantities worldwide—especially in polycarbonate plastics and as a polymer additive. Recently, some manufacturers have begun using alternative bisphenol compounds, such as bisphenol F (BPF) and bisphenol S (BPS). These uses of bisphenols have led to widespread bisphenol detections in the environment and wildlife. The present study examined wastewater effluent in the San Francisco Bay Area and San Francisco Bay sediment samples for 17 bisphenols. The effluent samples were compared to available stormwater runoff data to better understand bisphenol transport, fate, and potential risks to wildlife.

Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California

Harmful Algae (Elsevier) | March 10th, 2018

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

Brackish Water Desalination Facility Draft Environmental Impact Report

City of Antioch | June 15th, 2018

The City proposes to construct, operate, and maintain the Antioch Brackish Water Desalination Project (proposed project). The City proposes to replace the existing San J

The City proposes to construct, operate, and maintain the Antioch Brackish Water Desalination Project (proposed project). The City proposes to replace the existing San Joaquin River intake pump station, construct a desalination facility with associated equipment and appurtenances; and construction of pipelines for the conveyance of source water and brine concentrate. The desalination plant would have the capacity to produce up to 6 million gallons per day (mgd) of desalinated product water to offset use of purchased water. Due to size, this file has been divided into two parts. Part 1, Part 2

Brackish Water Desalination Facility Project

Delta Stewardship Council (Delta Council) | April 1st, 2020

The City of Antioch (City) is proposing the Brackish Water Desalination Project (Project), which consists of the construction of a desalination facility at the City’s

The City of Antioch (City) is proposing the Brackish Water Desalination Project (Project), which consists of the construction of a desalination facility at the City’s water treatment plant (WTP) with the capacity to produce up to 6 million gallons per day (mgd) of finished water; demolition of the existing San Joaquin River intake pump station; construction of a new intake pump station; approximately 3,000 feet of pipeline from the existing raw water pipeline underneath Lone Tree Way to the City’s WTP to allow a direct connection to maximize use of existing infrastructure; and approximately 4 miles of pipeline from the desalination facility to the Delta Diablo wastewater treatment plant (WWTP) to discharge brine with the WWTP effluent through the existing Delta Diablo outfall to New York Slough. The Project facilities would be located in the cities of Antioch and Pittsburg, California (Figure 1), at the western edge of the San Joaquin- Sacramento Delta (Delta). The main objectives of the Project are to improve water supply reliability and water quality for its customers; develop a reliable and drought-resistance water source to reduce dependency on purchased water supplies; maximize and preserve the use of the City’s pre-1914 water rights; and provide cost effective operational flexibility for the City.