San Francisco Bay

USGS Science at Work in the San Francisco Bay and Sacramento-San Joaquin Delta Estuary

U.S. Geological Survey (USGS) | ?

The San Francisco Bay and Sacramento-San Joaquin Delta form one of the largest estuaries in the United States. The “Bay-Delta” system provides water to more than 25 m

The San Francisco Bay and Sacramento-San Joaquin Delta form one of the largest estuaries in the United States. The “Bay-Delta” system provides water to more than 25 million California residents and vast farmlands, as well as key habitat for birds, fish, and other wildlife. To help ensure the health of this crucial estuary, the U.S. Geological Survey, in close cooperation with partner agencies and organizations, is providing science essential to addressing societal issues associated with water quantity and quality, sediment transportation, environmental contamination, animal health and status, habitat restoration, hazards, ground subsidence, and climate change.

Using Conceptual Models and Decision-Support Tools to Guide Ecosystem Restoration Planning and Adaptive Management: An Example from the Sacramento–San Joaquin Delta, California

University of California, Davis (UC Davis) | October 1st, 2012

The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. H

The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. However, ecosystem alterations for human uses changed many of the Delta’s natural processes, and it is now considered in need of restoration. An approach was developed to evaluate and rank restoration actions in the Delta under the Ecosystem Restoration Program’s Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The DRERIP approach provides an explicit framework for evaluating restoration actions, using linked conceptual models, an action evaluation procedure, and a decision-support tool. Conceptual models allow scientists and managers to synthesize scientific information and make qualitative predictions about ecosystem function and restoration outcomes to guide and focus restoration efforts. The action evaluation procedure is a structured assessment of restoration actions. The procedure clearly describes actions to be evaluated, assesses the magnitude (importance and scale) and certainty of anticipated ecological outcomes, estimates degrees of worth (achieving intended outcomes) and risk (causing adverse consequences), evaluates the reversibility of the action, and identifies opportunities for learning. The values for worthiness, risk, reversibility, and learning opportunity are used in the decision- support tool to determine the fate of a proposed action. The decision-support tool is a structured decision tree that determines the disposition of an action: whether a restoration project should be discarded, revised with a different approach and re-evaluated, or implemented; and, if implemented, at what scale (targeted research, pilot project, or full implementation). The DRERIP approach provides managers with a valuable tool for restoration planning, and a foundation for integration with quantitative methods for a comprehensive ecosystem restoration plan.

Valuing Urban Nature – Implications for Flood Resilience

Stanford University | June 3rd, 2019

Sea-level rise and extreme weather events such as torrential rain storms are having devastating consequences in the United States and globally. Researchers, prac

Sea-level rise and extreme weather events such as torrential rain storms are having devastating consequences in the United States and globally. Researchers, practitioners, and policymakers are increasingly calling for the use of natural and nature-based approaches to protect urban areas from flooding which has increased in frequency and intensity as a result. Natural features can help stabilize shorelines and protect communities from river flooding while, providing other co- benefits for people and ecosystems. In a new study, scientists at the Natural Capital Project developed a framework for valuating urban nature and examined different factors cities must consider when making infrastructure and other investment choices. This brief is part of a series based on that research which looks at nature’s abilityto provide resilience to flooding and the various co-benefits associated with nature-based solutions.

Variable coastal hypoxia exposure and drivers across the southern California Current

Nature Portfolio (Springer Nature) | May 25th, 2021

Declining oxygen is one of the most drastic changes in the ocean, and this trend is expected to worsen under future climate change scenarios. Spatial variability in disso

Declining oxygen is one of the most drastic changes in the ocean, and this trend is expected to worsen under future climate change scenarios. Spatial variability in dissolved oxygen dynamics and hypoxia exposures can drive differences in vulnerabilities of coastal ecosystems and resources, but documentation of variability at regional scales is rare in open-coast systems. Using a regional collaborative network of dissolved oxygen and temperature sensors maintained by scientists and fishing cooperatives from California, USA, and Baja California, Mexico, we characterize spatial and temporal variability in dissolved oxygen and seawater temperature dynamics in kelp forest ecosystems across 13° of latitude in the productive California Current upwelling system. We find distinct latitudinal patterns of hypoxia exposure and evidence for upwelling and respiration as regional drivers of oxygen dynamics, as well as more localized effects. This regional and small-scale spatial variability in dissolved oxygen dynamics supports the use of adaptive management at local scales, and highlights the value of collaborative, large-scale coastal monitoring networks for informing effective adaptation strategies for coastal communities and fisheries in a changing climate.

Variable vertical land motion and its impacts on sea level rise projections

American Association for the Advancement of Science (AAAS) | January 29th, 2025

Coastal vertical land motion (VLM), including uplift and subsidence, can greatly alter relative sea level projections and flood mitigations plans. Yet, current projection

Coastal vertical land motion (VLM), including uplift and subsidence, can greatly alter relative sea level projections and flood mitigations plans. Yet, current projection frameworks, such as the IPCC Sixth Assessment Report, often underestimate VLM by relying on regional linear estimates. Using high-resolution (90-meter) satellite data from 2015 to 2023, we provide local VLM estimates for California and assess their contribution to sea level rise both now and in future. Our findings reveal that regional estimates substantially understate sea level rise in parts of San Francisco and Los Angeles, projecting more than double the expected rise by 2050. Additionally, temporally variable (nonlinear) VLM, driven by factors such as hydrocarbon and groundwater extraction, can increase uncertainties in 2050 projections by up to 0.4 meters in certain areas of Los Angeles and San Diego. This study highlights the critical need to include local VLM and its uncertainties in sea level rise assessments to improve coastal management and ensure effective adaptation efforts.

Variations on a method for evaluating decadal-scale changes in the groundwater quality of two GAMA coastal study units 2004–14, California GAMA Priority Basin Project

U.S. Geological Survey (USGS) | August 8th, 2018

Decadal changes in groundwater quality in two study units on the north-central California coast were evaluated by the Priority Basin Project (PBP) of the Groundwater Ambi

Decadal changes in groundwater quality in two study units on the north-central California coast were evaluated by the Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. Groundwater samples collected from wells during 2004–05 were compared on a pair-wise basis to samples collected from the same wells during 2014. The data set consisted of paired-samples from 50 public supply wells in 2 GAMA-PBP study units (25 wells each in the North San Francisco Bay and the Monterey Bay and Salinas Valley Basins), with analytical results for 160 water-quality constituents. Statistical analysis was done on grouped results for the 59 constituents that were detected in at least 10 percent of the samples during either sampling period to evaluate decadal-scale change by a step-trend analysis. The data for both of the sampling periods were processed three different ways, resulting in three variations of the paired results to be submitted for statistical analyses. The first evaluation method variation processed data only to facilitate comparison of data when one or both of the results was a non-detection. The second and third variations applied the additional requirement that differences between initial and decadal-sample results exceed a defined threshold to prevent small differences from supporting the conclusion of a step trend. One method for setting the difference threshold between initial-sampling and resampling results is based on criteria used by the GAMA-PBP to determine whether or not replicate results are acceptable. The other difference-threshold-setting method uses a calculated confidence interval around each result based on demonstrated analytical variability for the constituents during each sampling period. Finally, constituents for which decadal-scale changes were statistically significant were identified using the Wilcoxon-Pratt signed-rank test on each of the three evaluation method variations. Step trends were identified by at least 1 of the 3 method variations for 33 constituents. After considering other factors, however, such as water-quality context and the results of quality-control samples, it was concluded that decadal changes were meaningful for 14 constituents in at least 1 of the 2 study units. Constituents for which step trends indicated meaningful increases were dissolved oxygen, total nitrogen, nitrate, orthophosphate, calcium, chloride, sulfate, iron, and lithium. Constituents for which step trends indicated meaningful decreases were temperature, arsenic, lead, the isotopic ratio of carbon-13, and tritium.

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