Ecological Studies of the Sacramento-San Joaquin Estuary, A Decennial Report 1961-1971

California Department of Fish and Wildlife (CDFW) | June 15th, 1972

Economic and water supply effects of ending groundwater overdraft in California’s Central Valley

University of California, Davis (UC Davis) | March 1st, 2016

Surface water and groundwater management are often tightly linked, even when linkage is not intended or expected. This link is especially common in semi-arid regions,

Surface water and groundwater management are often tightly linked, even when linkage is not intended or expected. This link is especially common in semi-arid regions, such as California. This paper summarizes a modeling study on the effects of ending long-term overdraft in California’s Central Valley, the state’s largest aquifer system. The study focuses on economic and operational aspects, such as surface water pumping and diversions, groundwater recharge, water scarcity, and the associated operating and water scarcity costs. This analysis uses CALVIN, a hydro-economic optimization model for California’s water resource system that suggests operational changes to minimize net system costs for a given set of conditions, such as ending long-term overdraft. Based on model results, ending overdraft might induce some major statewide operational changes, including large increases to Delta exports, more intensive conjunctive-use operations with increasing artificial and in-lieu recharge, and greater water scarcity for Central Valley agriculture. The statewide costs of ending roughly 1.2 maf yr-1  of groundwater overdraft are at least $50 million per year from additional direct water shortage and additional operating costs. At its worst, the costs of ending Central Valley overdraft could be much higher, perhaps comparable to the recent economic effects of drought. Driven by recent state legislation to improve groundwater sustainability, ending groundwater overdraft has important implications statewide for water use and management, particularly in the Sacramento–San Joaquin Delta. Ending Central Valley overdraft will amplify economic pressure to increase Delta water exports rather than reduce them, tying together two of California’s largest water management problems.

Economic Sustainability Plan for the Sacramento-San Joaquin Delta

Delta Protection Commission (DPC) | July 19th, 2012

The Sacramento-San Joaquin River Delta is a unique place of economic, environmental, historic, and cultural significance. The land and water resources of the Delta suppor

The Sacramento-San Joaquin River Delta is a unique place of economic, environmental, historic, and cultural significance. The land and water resources of the Delta support significant agricultural and recreation economies, and the Delta also has an important role as an infrastructure hub for water, energy, and transportation. The region’s rich history boasts of bustling, river-based commerce before the automobile age, and its cultural uniqueness includes the only rural town in America build by early Chinese immigrants. As the largest estuary on the west coast of the Americas, the Delta also is a place of striking natural beauty and ecological significance that is struggling with serious environmental degradation problems. Although surrounded by growing cities, the Delta remains a highly-productive agricultural area with rural charms, landscapes, and waterscapes not found elsewhere in California. In recent years, there has been great concern over increasing environmental degradation in the Delta and over court decisions that reduced the quantity of water delivered to southern California through the state and federal water project intakes in the south Delta to protect endangered fish. Combined with additional concerns about the stability of the Delta’s levee system, these concerns led the California legislature to pass the Delta Reform Act of 2009. The Act created the Delta Stewardship Council and charged it with developing a Delta Plan to achieve the coequal goals of “providing a more reliable water supply for California and protecting, restoring, and enhancing the Delta ecosystem.” Recognizing the potential impact of the Delta Plan on the people and economy of the Delta, the Delta Reform Act stated that the coequal goals of water supply reliability and restoring the Delta ecosystem “shall be achieved in a manner that protects and enhances the unique cultural, recreational, natural resource, and agricultural values of the Delta as an evolving place.” Among the measures to address this goal, the Delta Protection Commission was tasked with developing this Economic Sustainability Plan to inform the Delta Stewardship Council’s development of the Delta Plan. The Legislature established the following guidelines for the Economic Sustainability Plan in the Delta Reform Act of 2009: "The economic sustainability plan shall include information and recommendations that inform the Delta Stewardship Council’s policies regarding the socioeconomic sustainability of the Delta region. (b) The economic sustainability plan shall include, but not be limited to, all of the following: 1) Public safety recommendations, such as flood protection recommendations. 2) The economic goals, policies, and objectives in local general plans and other local economic efforts, including recommendations on continued socioeconomic sustainability of agriculture and its infrastructure and legacy communities in the Delta. 3) Comments and recommendations to the Department of Water Resources concerning its periodic update of the flood management plan for the Delta. 4) Identification of ways to encourage recreational investment along the key river corridors, as appropriate. Since a key purpose of this Economic Sustainability Plan is to inform the Delta Plan under development by the Delta Stewardship Council, this report analyzes the impact of key policies being considered for the plan on the economic sustainability of the Delta. Many of the most significant proposals for the Delta are being developed in the Bay Delta Conservation Plan (BDCP). The policy proposals can be grouped into four categories: 1) water conveyance, 2) habitat creation, 3) levees, and 4) land use regulation. The report also considers many aspects of economic sustainability in the Delta that are unrelated to these water policy proposals including economic development recommendations in the 2008 Delta Vision Strategic Plan.

Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay

Limnology and Oceanography (Wiley) | March 25th, 2017

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

Effect of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 15th, 2018

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary ro

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary rock-fill barriers constructed in waterways located in the southern portion of the Sacramento-San Joaquin Delta (Delta) near the cities of Tracy and Lathrop in San Joaquin County, California (Figure 1-1). Three of the temporary barriers—Old River at Tracy (ORTB), Middle River (MRB), and Grant Line Canal (GLCB), collectively, the south Delta agricultural barriers (SDABs)—are constructed and operated during the agricultural irrigation season, usually April through November. The SDABs are designed to act as flow control structures, retaining tidal fresh water behind each barrier following a flood tide. The fourth barrier, Head of Old River Barrier (HORB), is installed during the spring and fall as a fish guidance barrier. The HORB is normally installed in the spring to prevent juvenile fall-run San Joaquin River Chinook Salmon (Oncorhynchus tshawytscha) and juvenile Central Valley steelhead (Oncorhynchus mykiss) 2 from emigrating through Old River toward the south Delta water export facilities at the intakes of the State Water Project (SWP) and federal Central Valley Project (CVP). In the fall, the HORB helps to guide adult San Joaquin River Chinook Salmon to spawning locations in the upper watershed. Installation, operation, and removal of the SDABs has the potential to harm, harass, or cause mortality to fish species of management concern to the National Marine Fisheries Service (NMFS), specifically, juvenile fall-run Chinook Salmon which are NMFS Species of Concern (NMFS 2010), juvenile Central Valley steelhead which is a threatened species, an Endangered Species Act (ESA) Section 10j experimental population (63 Federal Register [FR] 13347), and juvenile Green Sturgeon (Acipenser medirostris), also a federally listed threatened species (71 FR 17757). The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009).

Effects of ferric sulfate and polyaluminum chloride coagulation enhanced treatment wetlands on Typha growth, soil and water chemistry

Science of the Total Environment (Elsevier) | January 15th, 2019

Land surface subsidence is a concern in many deltas worldwide as it contributes to water quality degradation, loss of fertile land and increased potential for levee f

Land surface subsidence is a concern in many deltas worldwide as it contributes to water quality degradation, loss of fertile land and increased potential for levee failure. As a possible solution to these concerns, on-site coagulation enhanced treatment wetlands (CETWs), coagulation water treatment followed by wetland passage serving as a settling basin, were implemented in a field-scale study located on a subsided island of the Sacramento-San Joaquin Delta in northern California under three treatments; coagulation with polyaluminum chloride (PAC), coagulation with ferric sulfate and an untreated control. Because CETWs offer a relatively novel solution for water quality improvement and subsidence reversal due to its low-infrastructure requirements and in-situ nature, effects from these systems remain uncharted and they may have adverse effects on plant biomass production that also contribute to sediment accretion. This study focuses on the effect CETWs had on the growth of Typha spp.; the dominant vegetation in the wetlands. Plant growth parameters and nutrient content were measured in conjunction with soil, pore water and surface water chemistry. Soil analysis indicated there was no intermixing of newly formed flocs and original soil material. Where there was significant deposition of floc, PAC treatment reduced phosphateconcentrations and ferric sulfate treatment increased total Fe concentrations in surrounding water compared to the control. Results indicated coagulation treatments had no negative effects on Typha leaf nutrient content, Typha growth or allometric parameters. Additionally, no signs of plant toxicity such as necrosis, wilting or chlorosis were observed in any of the treatments. Overall, this study suggests that CETWs are viable treatment option for water quality improvement and sediment accretion while having no negative impact on the growth of Typha plants.

Effects of flow on pesticides in water and zooplankton in the northern Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | November 1st, 2025

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.

Effects of Flow on Pesticides in Water and Zooplankton in the Northern Sacramento–San Joaquin Delta

University of California, Davis (UC Davis) | December 19th, 2025

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.

Effects of high temperatures on threatened estuarine fishes during periods of extreme drought

Journal of Experimental Biology (The Company of Biologists) | March 1st, 2016

Climate change and associated increases in water temperatures may impact physiological performance in ectotherms and exacerbate endangered species declines. We used an in

Climate change and associated increases in water temperatures may impact physiological performance in ectotherms and exacerbate endangered species declines. We used an integrative approach to assess the impact of elevated water temperature on two fishes of immediate conservation concern in a large estuary system, the threatened longfin smelt (Spirinchus thaleichthys) and endangered delta smelt (Hypomesus transpacificus). Abundances have reached record lows in California, USA, and these populations are at imminent risk of extirpation. California is currently impacted by a severe drought, resulting in high water temperatures, conditions that will become more common as a result of climate change. We exposed fish to environmentally relevant temperatures (14°C and 20°C) and used RNA sequencing to examine the transcriptome-wide responses to elevated water temperature in both species. Consistent with having a lower temperature tolerance, longfin smelt exhibited a pronounced cellular stress response, with an upregulation of heat shock proteins, after exposure to 20°C that was not observed in delta smelt. We detected an increase in metabolic rate in delta smelt at 20°C and increased expression of genes involved in metabolic processes and protein synthesis, patterns not observed in longfin smelt. Through examination of responses across multiple levels of biological organization, and by linking these responses to habitat distributions in the wild, we demonstrate that longfin smelt may be more susceptible than delta smelt to increases in temperatures, and they have little room to tolerate future warming in California. Understanding the species-specific physiological responses of sensitive species to environmental stressors is crucial for conservation efforts and managing aquatic systems globally.

Effects of Hydraulic Conditions on Salvage Efficiency of Adult Delta Smelt at the Tracy Fish Collection Facility

U.S. Bureau of Reclamation (USBR) | February 29th, 2016