San Joaquin River

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.

Detections of current-use pesticides at 12 surface water sites in California during a 2-year period beginning in 2015

U.S. Geological Survey (USGS) | July 27th, 2018

Surface water samples were collected by the U.S. Geological Survey and multiple cooperators during base flow/irrigation runoff and storm runoff conditions from 12 sites t

Surface water samples were collected by the U.S. Geological Survey and multiple cooperators during base flow/irrigation runoff and storm runoff conditions from 12 sites throughout California, over 2 consecutive years beginning in April 2015, from both urban and agriculturally dominated watersheds. Water samples were analyzed by gas chromatography/mass spectrometry and liquid chromatrography/tandem mass spectrometry for a suite of 157 pesticides and degradates. Suspended sediments associated with these water samples were analyzed by gas chromatography/mass spectrometry for a suite of 131 pesticides and degradates. Overall, 85 pesticides and degradates were detected in the water: 32 fungicides, 25 herbicides, 27 insecticides, and 1 synergist. In the suspended sediment, 29 pesticides were detected: 9 fungicides, 10 herbicides, and 10 insecticides. Sixteen pesticides (bifenthrin, carbendazim, chlorpyrifos, clothianidin, diazinon, diuron, fenpyroximate, fipronil, fipronil sulfone, fluopicolide, imidacloprid, metolachlor, novaluron, oxyflurofen, permethrin, and simazine) were detected in the water at concentrations that were above at least one aquatic life benchmark value as defined by the U.S Environmental Protection Agency.

Development and Application of a 1D Compaction Model to Understand 65 Years of Subsidence in the San Joaquin Valley

American Geophysical Union (AGU) | June 2nd, 2022

High rates of land subsidence, caused by groundwater overdraft, are resulting in millions of dollars of infrastructure damage in California's San Joaquin Valley (SJV). In

High rates of land subsidence, caused by groundwater overdraft, are resulting in millions of dollars of infrastructure damage in California's San Joaquin Valley (SJV). In recent years, the use of interferometric synthetic aperture radar (InSAR) has enabled us to substantially improve our understanding of this subsidence. However, only very occasionally have the InSAR data been integrated with a physical model of subsurface compaction. Here, we have used InSAR and other data to parameterize and calibrate a 1D compaction model. We applied our model to a study area in the SJV where we had access to the necessary information on hydraulic head to develop model inputs. Our model simulated subsidence in the three aquifer system layers over the period 1952–2017, and is the first 1D compaction model in the SJV to simulate multiple aquifer system layers from the 1950s to 2017. The results from our model suggest that previous studies have significantly underestimated the time constants governing the slow, residual compaction of subsurface clays. We suggest that residual compaction of clays is a process that continues for decades-to-centuries, indicating that to significantly reduce subsidence requires some recovery of head, not just a stabilization. We also show how compaction in the lower, confined aquifer has accounted for over 90% of subsidence in the past 20 years. Although our study area is small, our findings are likely representative of the subsiding regions of the SJV, and our methodology can be applied to unconsolidated aquifer systems exhibiting subsidence worldwide.

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

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.

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.

Distribution of Lakes in the United States

Scientific American | June 12th, 1880

There are numerous lacustrine basins to be found in the States bordering the Pacific Ocean. As in other regions of the globe, their distribution is determined by the co

There are numerous lacustrine basins to be found in the States bordering the Pacific Ocean. As in other regions of the globe, their distribution is determined by the configuration of land, or, more specifically, by the forms of the great hydrographic basins in the interior of the continent; hence some general idea of the topography of the western portions of the United States is an essential preliminary.