San Francisco Bay

Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act

National Marine Fisheries Service (NMFS) | July 25th, 2016

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five ye

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five years and determine whether any species should be removed from the list or have its listing status changed. Assessments of the viability of ESA-listed Pacific salmonids were conducted by the Southwest Fisheries Science Center and the Northwest Fisheries Science Center. The information from these assessments is incorporated into the West Coast Region’s status review, and the NMFS West Coast Region will make final determinations about any proposed changes in listing status, taking into account not only biological information (viability assessments) but also threats to the species and ongoing or planned protective efforts. This report from the Southwest Fisheries Science Center covers 10 ESA-listed Evolutionarily Significant Units (ESUs) and Distinct Population Segments (DPSs) that lie wholly or partially in California. In this review, we consider 1) new information relevant to the delineation of ESU/DPS boundaries, and 2) new information on status and trends in abundance, productivity, spatial structure and diversity specifically addressed by viability criteria previously developed by Technical Recovery Teams (TRTs). These viability assessments summarize current information (through the 2014–2015 spawning year where available) with respect to the viability criteria developed by the TRTs.  Consequently, the current assessments consider not only changes in populations that have occurred since the 2010 assessments but also the status of populations and ESUs/DPSs in relation to the viability criteria developed by the TRTs. For eight of the ESUs/DPSs (Southern Oregon/Northern California Coho Salmon, Central California Coast Coho Salmon, California Coastal Chinook Salmon, Northern California Steelhead, Central California Coast Steelhead, South-central California Steelhead, Southern California Steelhead, and California Central Valley Steelhead) the new information suggests that there has been no change in extinction risk since 2010 viability assessments. For two ESUs (Central Valley Spring-run Chinook Salmon, and Sacramento River Winter-run Chinook Salmon) the new information suggests a change in extinction risk. The viability of Central Valley Spring-run Chinook salmon appears to have improved since the 2010 assessment, but this ESU is far from being viable and is still facing relatively high extinction risk. The viability of Sacramento River Winter-run Chinook Salmon has been reduced and the ESU faces greater extinction risk since the 2010 assessment.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Nature Portfolio (Springer Nature) | December 1st, 2022

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in oto

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Vulnerability Assessments in Support of the Climate Ready Estuaries Program: A Novel Approach Using Expert Judgment, Volume I

U.S. Environmental Protection Agency (EPA) | January 1st, 2012

The San Francisco Bay estuary is highly vulnerable to climate - related changes including increased water temperatures, changes in precipitation and winds, and sea leve

The San Francisco Bay estuary is highly vulnerable to climate - related changes including increased water temperatures, changes in precipitation and winds, and sea level rise. Impacts such as increased inundation of coastal wetlands, changes in water availability and quality, and altered patterns of sedimentation and erosion are increasingly interacting with other human stressors such as extractive water uses and land use changes. Thus it is essential that estuary managers become ‘climate-ready’ by: assessing the vulnerability of natural resources to climate change; considering strategic choices among adaptation strategies in the near term; and engaging in longer term planning based on a range of plausible scenarios of future change. In an era of shrinking budgets coupled with increasingly complex decision-making needs—often taking place in a context of uncertainty and incomplete information— managing natural resources in the face of climate change will be challenging. There is a need for assessment methods that take advantage of existing scientific expertise to help identify robust adaptation strategies, weigh difficult trade-offs, and justify strong action, all in a timely and efficient manner. The purpose of this project was to carry out a pilot vulnerability assessment for the San Francisco Estuary Partnership’s (SFEP) natural resources using expert judgment, the results of which could be linked to adaptation planning. To this aim, EPA’s Office of Research and Development collaborated with SFEP and the San Francisco Bay Conservation and Development Commission on a novel expert elicitation exercise for ‘rapid’ vulnerability assessment. A trial exercise was carried out during a two-day workshop in which two groups of seven experts each focused on two key ecosystem processes: sediment retention in salt marshes and community interactions of shorebirds with their predators and prey (see Figure ES - 1). The exercise, which was based on formal expert elicitation techniques but tailored specifically for qualitative analysis of ecosystem processes, was designed to glean expert information on the sensitivities of ecosystem process components under future climate scenarios . This was followed by group discussions of the implications of the results for management in light of climate change, as well as feedback on the exercise itself.  

Water Accounting in Western US, Australia, and Spain: Comparative Analysis

American Society of Civil Engineers (ASCE) | January 10th, 2020

Water Allocation in California - Legal Rights and Reform Needs

Golden Gate University (GSU) | March 31st, 1982

FOREWARD: Water supply, allocation, use and conservation are constantly debated in California, often appearing as highly charged political issues in candidates' races and

FOREWARD: Water supply, allocation, use and conservation are constantly debated in California, often appearing as highly charged political issues in candidates' races and on election ballots. This year is no exception, with major ballot propositions already scheduled for the June primary election and being circulated to qualify for the November general election. Accordingly this Research Paper on legal aspects of water allocation is being published for the valuable background it affords readers wishing to learn more about the subject. The author draws on his legal expertise, as well as his experience as Staff Director of the Governor's Commission to Review California Water Rights Law. The paper emphasizes the crucial role of water rights in California water management, and it points to the need for and present lack of a political consensus on water law reform. The author concludes by suggesting forces that could bring about interest-group realignments and other developments favorable to achieving the needed consensus on water law and management reform that so far has eluded Californians. Stanley Scott Assistant Director Institute of Governmental Studies March 1982

Water and Energy in California

Public Policy Institute of California (PPIC) | December 6th, 2022

Water and Suspended-Sediment Flux Measurements at the Golden Gate, 2016-2017

San Francisco Estuary Institute (SFEI) | December 1st, 2017

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport an

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport and fate. Understanding the transport and fate of sediment in SFB is important to ecosystem researchers and managers. Previous studies have shown that sediment exchange at the estuary-ocean boundary of SFB (Golden Gate inlet) is the most poorly understood element of the SFB sediment budget, owing to logistical challenges that inhibit routine field observations, and the fact that net flux is a small fraction of the instantaneous peak values experienced on a daily basis. Improved understanding of sediment exchange at the estuary-ocean boundary of SFB is essential to updating SFB-wide sediment budgets, which account for sources, sinks, and storage of sediment (and sediment-associated contaminants). In this study, field observations of water and suspended-sediment fluxes at the Golden Gate were made over one ebb tide and one flood tide on three occasions: 1) 21-22 March 2016, following a large storm event that triggered the first flow into Yolo Bypass flood control structure since 2011 2) 23 June of 2016, during a period of low freshwater inflow; 3) 27-28 February 2017, following several large storms of the wettest winter in northern California in recorded history.

Water Available for Replenishment 2018

California Department of Water Resources (DWR) | April 12th, 2018

Water Column Selenium Concentrations in the San Francisco Bay-Delta: Recent Data and Recommendations for Future Monitoring

San Francisco Estuary Institute (SFEI) | August 1st, 2017

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 T

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 The TMDL is based on attainment of water column and fish tissue target concentrations protective of human health, aquatic life, and wildlife, and was approved by the US Environmental Protection Agency in August, 2016. Analyses in support of the TMDL synthesized the results of different monitoring efforts to characterize selenium concentrations in water and biota in the Estuary. For water quality evaluation in the TMDL, the sources of observational data included studies of selenium speciation across the estuarine salinity gradient, performed in 1999-2000 and again in 2010 and 2012 (Cutter and Cutter 2004, Doblin et al. 2006, Tetra Tech, 2012), as well as samples collected by the San Francisco Bay Regional Monitoring Program (RMP). Changes in wastewater treatment from the five major refineries in NSFB were implemented in the late 1990s, leading to significant reductions in selenium loads. Data at Estuary center-line locations showed small changes for dissolved selenium in the mid-salinity range and no trends in particulate selenium (Baginska, 2015). As part of the TMDL, water quality modeling analyses were performed to characterize NSFB selenium concentrations under a range of hydrologic conditions and changing point-source loads (Baginska, 2015). Water column selenium concentration data in the NSFB and Delta continue to be collected at selected locations, although these data have not been systematically evaluated following the analyses presented in the TMDL reports. In the near term, possible changes that may cause selenium concentrations to change in the NSFB and Delta include concentration changes in the inflow from the San Joaquin River basin, changes in refinery inputs, changes in stormwater and tributary loads from the Bay margin, and changes in overall Central Valley hydrological conditions, such as the extreme wet and dry periods that occurred between 2012 and 2017. Other drivers, such as nutrient concentrations and algal levels, may also play a role, especially on the concentrations of selenium on particulates.

Water Demand Projection Accuracy and Demand Management Trends in California Cities

American Geophysical Union (AGU) | November 21st, 2025

This study investigates the accuracy of long-term water demand projections and tracks the evolution of water demand management incentives across 61 California water suppl

This study investigates the accuracy of long-term water demand projections and tracks the evolution of water demand management incentives across 61 California water suppliers from 2000 to 2020. Through a systematic analysis of Urban Water Management Plans, we find that water suppliers consistently overestimated future demand by an average of 25% for 5-year projections and 74% for 20-year projections. This overestimation stems primarily from assumptions about per capita water demand rather than population growth estimates. While suppliers generally projected stable or increasing per capita demand, actual water demand per capita declined by 1.9% annually between 2000 and 2020, leading to a decoupling of water demand from population growth. Concurrently, we document a substantial increase in water demand management incentives, with non-voluntary regulations emerging as the dominant demand management approach by 2020, largely driven by state policies like the Model Water Efficient Landscape Ordinance and California Green Building Standards. Demand management efforts have evolved from primarily indoor and educational initiatives toward outdoor-focused non-voluntary regulations and rebates. This shift appears closely linked to the reduction in per capita demand that suppliers failed to fully capture in their water demand projections. Our findings underscore the importance of incorporating dynamic conservation trends into demand projections and suggest that suppliers should develop more sophisticated forecasting methods that account for the continuing evolution of water efficiency incentives. This research provides valuable insights for water resource planners seeking to improve the accuracy of water demand projections in an era of increasing conservation and climate uncertainty.