San Francisco Bay

Pesticide Concentrations Associated with Augmented Flow Pulses in the Yolo Bypass and Cache Slough Complex, California

U.S. Geological Survey (USGS) | July 23rd, 2020

Surface-water and suspended-sediment samples were collected and analyzed by the U.S. Geological Survey for multiple current-use pesticides and pesticide degradates approx

Surface-water and suspended-sediment samples were collected and analyzed by the U.S. Geological Survey for multiple current-use pesticides and pesticide degradates approximately every 2 weeks at up to five sites in the Yolo Bypass and Cache Slough Complex before, during, and after augmented flow pulses in summer and fall 2016 and 2018 as well as during ambient flow conditions in summer and fall 2017 (no flow pulse). In 2016, augmented flows occurred during the summer (July) and required the pumping of Sacramento River water by local Reclamation Districts into the Colusa Basin Drain and Yolo Bypass Toe Drain. In contrast, augmented flows in 2018 occurred in the fall (August–September) and used agricultural tailwater (primarily rice field discharge water) to create the flow pulse. Water samples were analyzed by the U.S. Geological Survey for a suite of 175 current-use pesticides and pesticide degradates using gas chromatography with mass spectrometry and liquid chromatography with tandem mass spectrometry laboratory methods. Suspended sediments filtered from the water samples were analyzed for 143 pesticides and degradates by gas chromatography with mass spectrometry. During the study, 53 pesticides were detected, and all the samples contained mixtures of multiple pesticides at concentrations ranging from below method detection limits to 8,780 nanograms per liter. Pesticides used in growing rice were the dominant pesticides present at four of the five sites sampled and urban-use pesticides dominated at the remaining site. Overall, total pesticide concentrations tended to be higher at sites in the northern part of the Yolo Bypass and lower at southern sites, except for the farthest downstream site which received additional pesticide inputs from the Sacramento River. Flow-pulse water source influenced total pesticide concentrations in the Yolo Bypass and Cache Slough Complex, and the highest total pesticide concentrations at each site were detected either immediately before or during the flow pulse generated with agricultural tailwater in 2018. Data gathered during this study will aid the California Department of Water Resources and other agencies working in the region in adaptively managing pulse flows in the Yolo Bypass and Cache Slough Complex, as one of several California Natural Resources Agency’s Delta Smelt Resiliency strategies.

Pesticide Mixtures in the Sacramento–San Joaquin Delta, 2016–17: Results from Year 2 of the Delta Regional Monitoring Program

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

Petaluma Valley Groundwater Sustainability Plan

Petaluma Valley Groundwater Sustainability Agency | December 8th, 2021

Due to size, this file has been divided Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7

Due to size, this file has been divided Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7

Petaluma Valley Historical Hydrology and Ecology Study

San Francisco Estuary Institute (SFEI) | March 1st, 2018

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over th

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over the past two centuries. Synthesizing information from hundreds of archival documents, the research reconstructs the historical form and function of wetland, riparian, and aquatic habitats and stream channels throughout the watershed, providing insights into habitat extent and distribution, streamflow and sediment dynamics, vegetation composition, wildlife support, and landscape change. Findings from this research can be used to help set restoration targets and to prioritize multi-benefit opportunities to restore wildlife habitat, enhance flood protection, increase groundwater recharge, and improve sediment management. This Executive Summary highlights key findings from the study. 

Petition for Extension of Time to Perfect Conditional Water Rights Under the State Water Project Permits (SWP) 16478, 16479, 16481, and 16482 for Water Supply and Permits 16477 and 16480 for Hydropower Operations

California Department of Water Resources (DWR) | January 21st, 2025

Click here for DWR press release and related correspondence.

Click here for DWR press release and related correspondence.

PFAS in San Francisco Bay Water

San Francisco Estuary Institute (SFEI) | November 14th, 2022

Per- and polyfluoroalkyl substances (PFAS), a family of thousands of synthetic, fluorine-rich compounds commonly referred to as “forever chemicals,” are known for the

Per- and polyfluoroalkyl substances (PFAS), a family of thousands of synthetic, fluorine-rich compounds commonly referred to as “forever chemicals,” are known for their thermal stability, non-reactivity, and surfactant properties. These unique compounds have widespread uses across consumer, commercial, and industrial products, resulting in widespread occurrence in the environment and wildlife across the globe. This study analyzed ambient surface water in San Francisco Bay for 40 PFAS to discern the occurrence, fate, and potential risks to ecological and human health.

Phase II: Alternative Courses of Action to Provide Delta Protection and Adequate Water Supplies for California

California Department of Water Resources (DWR) | March 15th, 1976

Phenomenological vs. biophysical models of thermal stress in aquatic eggs

Ecology Letters (Wiley) | January 1st, 2017

Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between

Predicting species responses to climate change is a central challenge in ecology. These predictions are often based on lab-derived phenomenological relationships between temperature and fitness metrics. We tested one of these relationships using the embryonic stage of a Chinook salmon population. We parameterised the model with laboratory data, applied it to predict survival in the field, and found that it significantly underestimated field-derived estimates of thermal mortality. We used a biophysical model based on mass transfer theory to show that the discrepancy was due to the differences in water flow velocities between the lab and the field. This mechanistic approach provides testable predictions for how the thermal tolerance of embryos depends on egg size and flow velocity of the surrounding water. We found support for these predictions across more than 180 fish species, suggesting that flow and temperature mediated oxygen limitation is a general mechanism underlying the thermal tolerance of embryos.

Physics to Fish: Understanding the Factors that Create and Sustain Native Fish Habitat in the San Francisco Estuary

U.S. Geological Survey (USGS) | January 16th, 2024

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to impro

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt (Hypomesus transpacificus) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid (Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California.

Phytoplankton, and Related Water-Quality Constituents in the California Sacramento– San Joaquin Delta at the Landscape Scale: 2018 High Resolution Mapping Surveys

U.S. Geological Survey (USGS) | April 1st, 2024

This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suis

This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suisun Bay, comprising three spatial surveys conducted in May, July, and October of 2018 that used continuous underway high frequency sampling and measurements onboard a high-speed boat to characterize spatial variation across the extent of the Delta. The method used involves simultaneously collecting information about the concentration and spatial distribution of all major nutrient forms with analogous information about the major classes of phytoplankton and associated water-quality conditions. The results showed substantial variation across space and time, providing an unprecedented snapshot of the dynamic environmental processes that shape the ways nutrients interact with and affect aquatic habitats in the Delta.