San Joaquin River

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

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.

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.

Physical Characteristics of the Lower San Joaquin River, California, in Relation to White Sturgeon Spawning Habitat, 2011–14

U.S. Geological Survey (USGS) | July 18th, 2017

The U.S. Fish and Wildlife Service confirmed that white sturgeon (Acipenser transmontanus) recently spawned in the lower San Joaquin River, California. Decreases in the S

The U.S. Fish and Wildlife Service confirmed that white sturgeon (Acipenser transmontanus) recently spawned in the lower San Joaquin River, California. Decreases in the San Francisco Bay estuary white sturgeon population have led to an increased effort to understand their migration behavior and habitat preferences. The preferred spawning habitat of other white sturgeon (for example, those in the Columbia and Klamath Rivers) is thought to be areas that have high water velocity, deep pools, and coarse bed material. Coarse bed material (pebbles and cobbles), in particular, is important for the survival of white sturgeon eggs and larvae. Knowledge of the physical characteristics of the lower San Joaquin River can be used to preserve sturgeon spawning habitat and lead to management decisions that could help increase the San Francisco Bay estuary white sturgeon population. Between 2011 and 2014, the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, assessed selected reaches and tributaries of the lower river in relation to sturgeon spawning habitat by (1) describing selected spawning reaches in terms of habitat-related physical characteristics (such as water depth and velocity, channel slope, and bed material) of the lower San Joaquin River between its confluences with the Stanislaus and Merced Rivers, (2) describing variations in these physical characteristics during wet and dry years, and (3) identifying potential reasons for these variations. The lower San Joaquin River was divided into five study reaches. Although data were collected from all study reaches, three subreaches where the USFWS collected viable eggs at multiple sites in 2011–12 from Orestimba Creek to Sturgeon Bend were of special interest. Water depth and velocity were measured using two different approaches—channel cross sections and longitudinal profiles—and data were collected using an acoustic Doppler current profiler. During the first year of data collection (water year 2011), runoff was greatest, and gaged streamflow, measured as discharge, peaked at 875 cubic meters per second in the lower San Joaquin River. Also during that year, water velocity was generally between 0.6 and 0.9 meters per second, and depth was typically between 2.5 and 4.5 meters, but water depth exceeded 6 meters in several pools. Water year 2011 was classified as a “wet” year. Later water years were classified as either “dry” (water year 2012) or “critical” (water years 2013 and 2014). During the drier years, water was shallower, and velocities were slower. The streambed aggraded in several areas during the study. At Sturgeon Bend, for example, which had the deepest pool measured in 2011 (maximum depth was 14 meters), about 8 meters of sediment was deposited by 2014. The bed of the lower San Joaquin River was predominately sand, except in areas downstream from the mouth of Del Puerto Creek. A large amount of sand, gravel, and cobble was deposited at the mouth of Del Puerto Creek, and in the 9.5 kilometers downstream from the mouth of Del Puerto Creek, we encountered several gravel bars and patches of gravel-size (8–64 millimeters) bed material. Del Puerto and Orestimba Creeks drain from the Coast Ranges on the west side of the river. Only small quantities of gravel-size bed material were observed in the reach downstream from Orestimba Creek, indicating Orestimba Creek does not deliver much coarse sediment to the lower San Joaquin River. Del Puerto Creek appeared to be the primary source of gravels suitable for white sturgeon spawning in the lower San Joaquin River, and thus, it is important for the long-term spawning success of sturgeon in the San Joaquin River.

Physical water system consolidation alone cannot resolve drinking water failure in California’s San Joaquin Valley

Nature Portfolio (Springer Nature) | July 2nd, 2026

Small community water systems in California’s San Joaquin Valley disproportionately fail to provide safe drinking water, with most serving disadvantaged communities and

Small community water systems in California’s San Joaquin Valley disproportionately fail to provide safe drinking water, with most serving disadvantaged communities and lacking the technical, managerial, and financial capacity to maintain compliance. The State Water Board designates such systems as failing when they have documented violations of drinking water standards or cannot reliably deliver safe water. Physical consolidation, which involves connecting a smaller failing system to a larger provider through new pipeline infrastructure, is the primary long-term solution promoted by state regulators. Here, we assess consolidation feasibility and capital costs across four counties (Kern, Kings, Tulare, and Fresno) via the state’s 2024 screening methodology. The methodology identifies smaller failing and at-risk systems as candidates for joining a larger receiving system with sufficient capacity. Among the 210 eligible systems, 114 (54%) matched a receiving system within three miles, with an estimated total capital need of $413.5 million. Nearly all identified pairs met state funding viability thresholds. The remaining 96 systems, including 49 classified as failing, lacked an eligible receiving partner and will require alternative solutions. Physical consolidation is necessary but insufficient for achieving safe drinking water access across the region.

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.

Pilot Study Examining Spatial Differences in Water Quality Between Shoal and Channel Habitats

San Francisco Estuary Institute (SFEI) | August 1st, 2019

Under the umbrella of the Nutrient Management Strategy (NMS; www.sfbaynutrients.sfei.org), we are investigating relationships between the SFB’s elevated nutrient levels

Under the umbrella of the Nutrient Management Strategy (NMS; www.sfbaynutrients.sfei.org), we are investigating relationships between the SFB’s elevated nutrient levels and phytoplankton production, with the goal of identifying protective nutrient loads and effective nutrient management options. To address these goals, NMS work includes continued ship-based monitoring (in collaboration with USGS); augmenting that monitoring with high-frequency sensor data and intensive field studies; and developing coupled hydrodynamic-biogeochemical models -- calibrated using field observations -- to simulate water quality under a range of forcings.