San Francisco Bay

Designing a High-Frequency Nutrient and Biogeochemical Monitoring Network for the Sacramento–San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the third in a series of three reports that provide information about how high-frequency (HF) nutrient monitoring may be used to assess nutrient inputs and

This report is the third in a series of three reports that provide information about how high-frequency (HF) nutrient monitoring may be used to assess nutrient inputs and dynamics in the Sacramento–San Joaquin Delta, California (Delta). The purpose of this report is to provide the background, principles, and considerations for designing an HF nutrient-monitoring network for the Delta to address high-priority, nutrient-management questions. The report starts with discussion of the high-priority management questions to be addressed, continues through discussion of the questions and considerations that place demands and constraints on network design, discusses the principles applicable to network design, and concludes with the presentation of three example nutrient-monitoring network designs for the Delta. For three example network designs, we assess how they would address high-priority questions that have been identified by the Delta Regional Monitoring Program (Delta Regional Monitoring Program Technical Advisory Committee, 2015). This report, along with the other two reports of this series (Kraus and others, 2017; Downing and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta. The first report in the series (Kraus and others, 2017) provides an introduction to the reasons for and fundamental concepts behind using HF monitoring measurements, including a brief summary of nutrient status and trends in the Delta and an extensive literature review showing how and where other research and monitoring programs have used HF monitoring to improve our understanding of nutrient cycling. The report covers the various technologies available for HF nutrient monitoring and presents the different ways HF monitoring instrumentation may be used for both fixed station and spatial assessments. Finally, it presents numerous examples of how HF measurements are currently (2017) being used in the Delta to examine how nutrients and nutrient cycling are related to aquatic habitat conditions.

Designs for cyanobacterial harmful algal bloom monitoring in the Sacramento–San Joaquin Delta, California

ESS Open Archive | December 5th, 2025

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and public health threats due to the production of potent cyanotoxins. The Sacramento–San Joaquin Delta (the Delta) has experienced CHABs since 1999, including CHABs that produce cyanotoxins at concentrations exceeding recreational advisory threshold levels. The report also describes how data from monitoring can be used to support model development to address management needs.

Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem

California State Water Resources Control Board (SWRCB) | August 4th, 2010

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 20

Water Code section 85086 (See Appendix B), contained in the Delta Reform Act, was enacted as part of the comprehensive package of water legislation adopted in November 2009. Water Code section 85086 requires the State Water Resources Control Board (State Water Board) to use the best available scientific information gathered as part of a public process conducted as an informational proceeding to develop new flow criteria for the Delta ecosystem to protect public trust resources. The purpose of the flow criteria is to inform planning decisions for the Delta Plan and the BDCP. The Legislature intended to establish an accelerated process to determine the instream flow needs of the Delta in order to facilitate the planning decisions required to meet the objectives of the Delta Plan. Accordingly, Water Code section 85086 requires the State Water Board to develop the flow criteria within nine months of enactment of the statute and to submit its flow criteria determinations to the Council within 30 days of their development. This report, required by Water Code section 85086(c) (2009 Delta Reform Act) in 2010, suggests the flows that would be needed in the Delta ecosystem if fishery protection was the sole purpose for which its waters were put to beneficial use. In keeping with the narrow focus of the legislation, this report only presents a technical assessment of flow and operational requirements to provide fishery protection under existing conditions.  

Development of Stage-Frequency Curves in the Sacramento-San Joaquin Delta for Climate Change and Sea Level Rise

California Energy Commission (CEC) | August 27th, 2018

Future changes in hydrologic patterns and sea level rise will impact water levels in the Sacramento-San Joaquin Delta (Delta), the hub of California’s water supply sys

Future changes in hydrologic patterns and sea level rise will impact water levels in the Sacramento-San Joaquin Delta (Delta), the hub of California’s water supply system and an important ecosystem and agricultural area. An important tool for flood management is stage frequency curves which indicate how often certain water levels (or stage) occur. The Delta poses inherent complexity in the determination of stage-frequency and requires a number of considerations. One needs to account for river flows coming into the Delta, as well as the effect of tides from the Delta’s connection to the ocean through San Francisco Bay. During storms, Delta water levels are also affected by storm surge from the advancing storm fronts coming from the Pacific Ocean. Under climate change, Delta water levels will also be affected by rising sea levels and expected changes in hydrology, such as shifts in timing and amount of precipitation and runoff and changes in how much of our precipitation falls as rain or snow (referred to as climate change hydrology in this paper). With these taken into consideration, this study lays out the assumption and method used to develop stage-frequency curves in the Delta for three different conditions: current hydrology conditions, current hydrology with sea level rise, and late-century climate change hydrology with sea level rise. In addition, water surface elevation profiles along the Sacramento and San Joaquin rivers for various magnitudes of flood events were compared to the top of levee elevations. Both the stage-frequency curves and the water surface elevation profiles comparisons to top of levee elevations provide valuable information to water resources planners and were applied to inform life and flood risk analysis for the Delta in the Central Valley Flood Protection Plan 2017 Update.

Dimension reduction approach for understanding resource-flow resilience to climate change

Nature Portfolio (Springer Nature) | June 15th, 2024

Dioxin Issue Paper: Expert Panel Response and Recommendations

Bay Area Clean Water Agencies (BACWA) | February 11th, 2010

Congeners of dioxins and furans have been found in the San Francisco Bay in several species of fish sometimes used for human consumption, causing the State of California

Congeners of dioxins and furans have been found in the San Francisco Bay in several species of fish sometimes used for human consumption, causing the State of California to issue an interim fish consumption advisory. This fish consumption advisory has been used by the US Environmental Protection Agency and the State of California as a basis for placing the Bay on the State’s list of impaired waterways required by the Clean Water Act. As a consequence, water quality-based discharge limits for dioxins are now being placed into NPDES permits for dischargers to the Bay where dioxins or furans have been detected in effluents. At the request of the Bay Area Clean Water Agencies (BACWA), an association of municipal wastewater treatment utilities, the San Francisco Estuary Institute convened a panel of three qualified experts to review the factual case and to make recommendations. As a starting point, BACWA prepared a draft “Dioxin Issue Paper” on February 15, 2008, detailing the environmental problem, the regulatory context, and the specific  difficulties presented by dioxin-related effluent limits in permits. The draft Dioxin Issue Paper also outlined an array of possible regulatory strategies which might help resolve the difficulties faced by dischargers, ranging from strategies related to impairment listing to strategies related to NPDES permit issuance. Panel members were asked to review the draft Dioxin Issue Paper, make recommendations for improvement, and respond to a number of questions posed by the San Francisco Estuary Institute. The Panel met in Oakland, California, on February 22, 2008, at the San Francisco Estuary Institute. We were joined by representatives of the San Francisco Bay Regional Water Quality Control Board, the US Environmental Protection Agency, BACWA, and others with expertise in the field. Subsequently, we held numerous conference calls and agreed that we would address the questions posed by the Institute in both short- and long-term contexts. For the short term, we agreed upon recommendations that could help alleviate some of the dioxin-related regulatory difficulties faced by municipal wastewater treatment plants. For the long-term, however, we agreed that the problems faced by the dischargers are best addressed by solutions for the dioxin contamination problems in the Bay as a whole. We therefore also agreed to recommend a series of steps towards developing an integrated multi-media strategy for reducing dioxin levels in the San Francisco Bay.

DISB Review of the Final EIR/EIS for California WaterFix

Delta Stewardship Council (Delta Council) | June 19th, 2017

The Delta Reform Act of 2009 directs the Delta Independent Science Board to review environmental impact assessments of the Bay Delta Conservation Plan (now California Wat

The Delta Reform Act of 2009 directs the Delta Independent Science Board to review environmental impact assessments of the Bay Delta Conservation Plan (now California WaterFix). Here, in our fifth such review, we focus on the adequacy of the scientific information presented in the final Environmental Impact Report (EIR)/Environmental Impact Statement (EIS) for the California WaterFix by revisiting the six main concerns we raised in our September 2015 review of the Recirculated Draft EIR/Supplemental EIS. We discuss improvements and shortcomings. We also comment on the need to improve impact assessments for scientific evaluation and effective stakeholder engagement. The Final EIR/EIS contains a wealth of detail and considerable insight. This version improves on its predecessors but retains some persistent shortcomings. Improved content on adaptive management is still short on detail about how adaptive management would be implemented under changing and uncertain conditions. Summaries and comparisons, more abundant than before, lack insightful syntheses and graphics that ease comprehension of the vast amount of material presented. Expanded discussion of Delta levees stops short of evaluating interactions with water supply reliability and neglects changing views of earthquake hazards. Long-term effects are better addressed in several ways, but with insufficient attention to uncertainties in defining the No Action Alternative and to the interplay between California groundwater sustainability and Delta water supplies. Other content missing includes evaluation of environmental effects of water use south of the Delta. Evaluation of ecosystem impacts, though extensive, retains gaps on using restoration as mitigation. The completion of our reviews of the Final EIR/EIS and its predecessors prompt us to reflect more broadly on the use and communication of science in the Delta and more specifically on the false trade off between thoroughness and intelligibility that has become common in environmental impact assessments. Overwhelming readers with content that addresses the many scientific issues related to a proposed project and its alternatives, while neglecting the thoughtful presentation and synthesis of insights and performance trade offs among alternatives, diminishes the value of this important document as a comparative guide to the expected environmental effects of the alternatives considered.

Disentangling Stationary and Dynamic Estuarine Fish Habitat to Inform Conservation: Species-Specific Responses to Physical Habitat and Water Quality in San Francisco Estuary

American Fisheries Society (AFS) | October 12th, 2021

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, wh

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidate how stationary (i.e., wetlands, shoals, and channels) and dynamic (i.e., salinity, temperature, turbidity, and chlorophyll concentration) habitat features interact to drive distributions of individual fish species. The Pacific coast of the conterminous United States has over 400 estuaries of various types. The largest (historical surface area) is San Francisco Estuary, California. We conducted extensive field observations of fishes in the central San Francisco Estuary among stationary habitat types (i.e., wetland, shoal, and channel) over a 19-month period encompassing substantial variability in dynamic water quality conditions. Most of the species observed, especially native species of special management interest, were associated with tidal wetland habitat. Few species exhibited associations with water quality conditions driven by seasonal (temperature) or a combination of broad- and fine-scale ecosystem processes (salinity and turbidity). Our study provides (1) an empirical demonstration of how researchers can deal with the complex and dynamic expressions of habitat in estuarine systems to address urgent natural resource problems and (2) a clear demonstration of the urgent need for habitat restoration and its likely outcome in systems such as San Francisco Estuary. Restoration of suitable tidal wetland habitat on the West Coast of the United States is likely to be an effective conservation tool to support estuarine fishes given that over 90% of historical tidal wetland habitat in San Francisco Estuary and 85% of vegetated wetland habitat along the Pacific coast of the United States has been lost due to human modification.

Dispersion and Stratification Dynamics in the Upper Sacramento River Deep Water Ship Channel

University of California, Davis (UC Davis) | December 1st, 2021

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosyste

Hydrodynamics control the movement of water and material within and among habitats, where time-scales of mixing can exert bottom-up regulatory effects on aquatic ecosystems through their influence on primary production. The San Francisco Estuary (estuary) is a low-productivity ecosystem, which is in part responsible for constraining higher trophic levels, including fishes. Many research and habitat-restoration efforts trying to increase primary production have been conducted, including, as described here, a whole-ecosystem nutrient addition experiment where calcium nitrate was applied in the Sacramento River Deep Water Ship Channel (DWSC) to see if phytoplankton production could be increased and exported out of the DWSC. As an integral part of this experiment, we investigated the physical mechanisms that control mixing, and how these mechanisms affect the strength and duration of thermal stratification, which we revealed as critical for controlling phytoplankton dynamics in the relatively turbid upper DWSC. Analysis of a suite of mixing mechanisms and time-scales show that both tidal currents and wind control mixing rates and stratification dynamics in the DWSC. Longitudinal and vertical dispersion increased during periods of high wind, during which wind speed influenced dispersion more than tidal currents. Thermal stratification developed most days, which slowed vertical mixing but was rapidly broken down by wind-induced mixing. Stratification rarely persisted for longer than 24 hours, limiting phytoplankton production in the study area. The interaction between physical mechanisms that control mixing rates, mediate stratification dynamics, and ultimately limit primary production in the DWSC may be useful in informing habitat restoration elsewhere in the Delta and in other turbid aquatic environments.

Dissolved Oxygen in South San Francisco Bay: Variability, Important Processes, and Implications for Understanding Fish Habitat

San Francisco Estuary Institute (SFEI) | October 30th, 2018

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Inst

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Institute (SFEI) launched a study to investigate the potential effects of low-DO on habitat quality in Lower South Bay (LSB) to inform decisions about nutrient regulation. The goal of the study was to understand where and when regions of LSB provide adequate DO to support resident fish species. The study approach involved convening a team of experts to advise on methods, analyzing high frequency DO measurements from seven mooring stations in LSB, and partnering with researchers from UC Davis to interpret several years of monthly fish abundance data in LSB relative to DO and other factors.