San Francisco Bay

National Marine Fisheries Service Biological Opinion for the Long-Term Operations of the Central Valley Project and State Water Project

National Marine Fisheries Service (NMFS) | June 3rd, 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.

Native and alien fishes in a California estuarine marsh: twenty-one years of changing assemblages

American Fisheries Society (AFS) | September 30th, 2002

We used monthly otter trawling and beach seining to sample the fishes of Suisun Marsh in the San Francisco Estuary from 1979 to 1999. We collected nearly 173,000 fish, mo

We used monthly otter trawling and beach seining to sample the fishes of Suisun Marsh in the San Francisco Estuary from 1979 to 1999. We collected nearly 173,000 fish, mostly young of the year, representing 28 native species and 25 alien species. Catch data were related to temperature, salinity, water transparency, and several measures of freshwater inflow into the marsh. Species abundance and distribution within the marsh were the product of several interacting factors: (1) the timing and place of reproduction of the abundant resident species, (2) past reproductive success, (3) habitat differences among sloughs, and (4) physiological tolerance. We did not find consistent groups of potentially interacting species, although some native species showed weak concordance in abundance. The lack of persistent fish assemblages is related to the naturally fluctuating environmental conditions of the estuary, the overall decline in fish abundance through time, and the frequent invasions of alien fishes and invertebrates. Our results suggest that the fish assemblages in Suisun Marsh will continue to be unpredictable until estuarine processes approach their historic range of variability and alien invasions are halted.

Natural Resources Defense Council v. Kempthorne, Order Granting in Part and Denying in Part Plaintiffs’ Motion for Summary Judgment

United States District Court, Eastern District of California | May 7th, 2007

This case concerns the effect on a threatened species of fish, the Delta smelt (Hypomesus transpacificus) , of the coordinated operation of the federally managed Central

This case concerns the effect on a threatened species of fish, the Delta smelt (Hypomesus transpacificus) , of the coordinated operation of the federally managed Central Valley Project ("CVP") and the State of California's State Water Project *2 ("SWP"), among the world's largest water diversion projects. Both projects divert large volumes of water from the California Bay (Sacramento - San Joaquin) Delta ("Delta") and use the Delta to store water.

Nature-based solutions extend the lifespan of a regional levee system under climate change

Nature Portfolio (Springer Nature) | May 9th, 2025

Near-Field Receiving-Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California

U.S. Geological Survey (USGS) | November 6th, 2019

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica), clam reproductive activity, and benthic macroinvertebrate co

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2018 to December 2018. These append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2018 data within the context of the longer, multi-decadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving-Water Monitoring Program, initiated in 1994. Significant reductions in silver and copper concentrations in both sediment and M. petalum occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized at concentrations somewhat above (silver [Ag]) or near (copper [Cu]) regional background concentrations. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2018, concentrations of silver and copper in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se, were generally similar in timing and magnitude as those for Ag and Cu. This record suggests that legacy contamination and regional-scale factors now largely control sedimentary and bioavailable concentrations of silver and copper, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in south San Francisco Bay over a 40-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum, from the same area. Analysis of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2018), with almost all animals initiating reproduction in the fall and spawning the following spring. The entire infaunal community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that indicates a more stable community that is subjected to fewer stressors. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that brood their young and live on the surface of the sediment in tubes have shown a continual decline in dominance coincident with the decline in metals; both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2018. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 numbers in 2018. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for deep-dwelling animals like M. petalum. However, within two months of this event, animals returned to the mudflat. The resilience of the community suggested that the disturbance was not caused by a persistent toxin or anoxia. The reproductive mode of most species that were present in 2018 was indicative of species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2018 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, have pelagic larvae that must survive landing on the sediment, and those that brood their young. USGS scientists view the 2008 disturbance event as a response by the infaunal community to an episodic natural stressor (possibly sediment accretion or a pulse of freshwater), in contrast to the long-term recovery from metal contamination. We will compare this recovery to the long-term recovery observed after the 1970s when the decline in sediment pollutants was the dominating factor.

Nearly a Million Californians Lack Access to Safe Drinking Water

State of California | July 26th, 2022

Our audit of the State Water Board’s efforts to help provide Californians with safe drinking water highlighted the following: More than 370 of the State’s water

Our audit of the State Water Board’s efforts to help provide Californians with safe drinking water highlighted the following: More than 370 of the State’s water systems, serving nearly a million Californians, exceed the maximum contaminant levels for substances that are harmful to human health. More than 150 of these systems have been failing for at least five years. Hundreds of additional water systems are currently at risk of failing. The State Water Board has not prioritized the processing of water systems’ funding applications so that the systems can improve their water quality. Over the past five years, the average length of time for water systems to complete their applications and receive funding nearly doubled, from 17 months to 33 months. The State Water Board has not established performance goals or metrics related to its cumbersome application process. Although the State Water Board provides water systems with technical assistance to plan their improvements and apply for funds, it has not adequately monitored the performance of the technical assistance providers with which it contracts. The State Water Board needs to better ensure that its staff and its contracted providers do not duplicate each other’s outreach efforts.

Necessity for Comprehensive Adjudication of Water Rights on the Sacramento and San Joaquin Rivers in Aid of the Central Valley Project

U.S. Government Publishing Office (GPO) | November 30th, 1942

Neonicotinoids and their Degradates in San Francisco Bay Water

San Francisco Estuary Institute (SFEI) | July 1st, 2020

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) screened Bay waters for neonicotinoid pesticides, comparing levels to toxicity thresholds to

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) screened Bay waters for neonicotinoid pesticides, comparing levels to toxicity thresholds to inform placement of this class of emerging contaminants within the tiered risk-based framework. Neonicotinoids are one of the most widely used classes of insecticides in the world. Given their widespread use in agricultural and urban environments, and ubiquitous detections in surface waters, there is growing concern about consequences for non-target species such as aquatic invertebrates, insects, birds, and fish. In the summer of 2017, open Bay water samples were collected during the RMP Status and Trends Water Cruise. Samples were analyzed for 19 neonicotinoids and metabolites. The only neonicotinoid detected was imidacloprid, an active ingredient used in both urban and agricultural applications. Imidacloprid was detected at a single site above the method detection limits (2.2-2.6 ng/L) in Lower South Bay at a level of 4.2 ng/L. This value is within the range of concentrations found in a separate RMP study in water samples collected from the South and Lower South Bay margins in 2017. Imidacloprid was detected at 3 of 12 of the margin sites at levels between 3.9 and 11 ng/L; no other neonicotinoids were detected. Of note, these RMP studies appear to represent the first evaluation of ambient neonicotinoid concentrations in an estuarine environment in the nation. Two significant pathways of imidacloprid contamination to the Bay are treated wastewater and runoff from the surrounding, primarily urban landscape. Previous RMP monitoring of wastewater influent and effluent, consisting of 24-hour composite samples collected from eight wastewater treatment facilities in the Bay Area in September 2015, detected imidacloprid in 100% of samples at levels up to 310 ng/L. Independent surveys in both northern and southern California urban areas confirm that imidacloprid is a commonly detected insecticide in urban runoff. For example, a San Francisco Bay Area study in Fairfield and Suisun City detected imidacloprid at up to 1,462 ng/L in urban creek waters. However, these concentrations diminished to below detection limits in downstream samples as creek waters mixed with brackish waters from the Bay. While Bay Area agricultural runoff has not been well-characterized with respect to imidacloprid, this pathway may also be of potential interest. A hydrodynamic dilution spreadsheet model was applied as an additional screening tool to explore predicted spatial patterns and temporal trends in imidacloprid concentrations in Bay subembayments. Model inputs were based on available data on concentrations in wastewater effluent and runoff. The model predicted that Lower South Bay levels of imidacloprid would be higher than in other subembayments. The Lower South Bay was also the only subembayment where imidacloprid concentrations were consistently predicted to be higher than method detection limits. The model indicated that wastewater was a dominant pathway for imidacloprid. However, stormwater discharges during the wet season could potentially lead to higher levels in the Bay, suggesting that dry season monitoring may not fully capture maximum concentrations. The results of this simplified dilution model are based on limited input data and do not include all relevant processes and removal mechanisms; they should be interpreted with caution and best viewed as a first step toward quantifiable prediction of open Bay concentrations. Open Bay and margins monitoring of imidacloprid revealed that detected concentrations in Lower South Bay were comparable to or greater than protective US and European Union thresholds that range from 4.8 to 10 ng/L. These observations, in combination with widespread and increasing use of this pesticide in urban settings, indicate that this contaminant should be classified as a Moderate Concern in the RMP tiered risk-based framework for contaminants of emerging concern. Other neonicotinoid pesticides and degradates should be classified as Possible Concern, given their more limited availability in urban use pesticide products, as well as additional uncertainties, particularly the lack of chronic toxicity data and potential for cumulative impacts to wildlife. Additional monitoring is not recommended at this time, due to existing monitoring in urban streams conducted primarily by the California Department of Pesticide Regulation (CDPR). In the future, it may be appropriate for the RMP to explore opportunities for wet season monitoring in Bay water, or in urban runoff. Considering the low toxicity thresholds of these compounds (i.e., in the low ng/L range), analytical methods employed should be improved to provide method detection limits well below toxicity thresholds.

New and Emerging Technologies for Sustainable Fisheries: A Comprehensive Landscape Analysis

Environmental Defense Fund (EDF) | April 1st, 2021

The oceans are at an inflection point. The excesses of the 20th century — over-exploitation of most of our accessible biological resources, over-pollution by plastics a

The oceans are at an inflection point. The excesses of the 20th century — over-exploitation of most of our accessible biological resources, over-pollution by plastics and other chemicals, over-crowding of coastal and marine space by unorganized and competing interests and over-capitalization of extractive industries — are being tempered by a rapidly growing realization that these excesses are having very real consequences, not just for marine life and ocean ecosystems, but for the food security and nutrition of the world’s population, the livelihoods of the communities that depend on the ocean and the very future of humanity itself. 

New Life for Eroding Shorelines: Beach and Marsh Edge Change in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | April 1st, 2020

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary sho

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary shoreline is relatively new; 15,000 years ago, the California shoreline was west of the Farallon Islands and 140 meters below its current level (Cohen and Laws 1992, Malamud-Roam et al. 2007). By approximately 6,000 years ago (the end of the last glacial epoch), the sea had risen to nearly its present level and filled what is now San Francisco Bay, allowing marshes to form and maintain themselves (Atwater 1979). More recently, humans have changed the shape of the shoreline. During the 1850s, many marshes expanded extensively due to increased sediment supply from hydraulic mining in the Sierra Nevada (Gilbert 1917, Goals Project 1999). Diking, dredging, and filling of marshes for agricultural and urban development began in the late 19th century and continued through the first half of the 20th century.  Today, humans continue to reshape the shoreline through continued diking, dredging and filling as well as restoration projects, urbanization of watersheds, ferry wakes, and many other means. The most wide-ranging impact of human activity on the shape of shorelines is global climate change caused by greenhouse gas emissions, which is accelerating the rate of sea level rise worldwide (OPC 2018). Sea level rise is likely to cause much more dramatic changes in the shape of shorelines than have been seen in recent centuries. The magnitude and pace of change will depend on the rate of sea level rise, existing shoreline conditions, and the ability of shorelines to adapt.