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

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

Eel River Restoration and Conservation Plan

California Trout | June 30th, 2024

This Eel River Restoration and Conservation Plan (Plan) will build on ... opportunities to guide substantial, collaborative, and long-term restoration and conservation ac

This Eel River Restoration and Conservation Plan (Plan) will build on ... opportunities to guide substantial, collaborative, and long-term restoration and conservation actions to revitalize the Eel River and restore its fisheries. In addition, the Plan has been prepared to expand and coordinate efforts among those who are working on restoration and conservation efforts in the basin to have the greatest effect toward recovery of native anadromous fish populations.

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 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 Groundwater Pumping on Agricultural Drains in the Tule Lake Subbasin, Oregon and California

U.S. Geological Survey (USGS) | July 24th, 2015

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from irrigation use to instream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation’s Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. U.S. Geological Survey regional groundwater-flow model simulations and records of irrigation-return flow pumped from the Tule Lake subbasin into the adjacent Lower Klamath Lake subbasin have indicated that water-level declines from pumping may be causing decreased flow of shallow groundwater to agricultural drains. To better define the effect of increased pumping on drain flow and on the water balance of the groundwater system, the annual water volume pumped from drains in three subareas of the Tule Lake subbasin was estimated and a fine-grid, local groundwater model of the Tule Lake subbasin was constructed. Results of the agricultural-drain flow analysis indicate that groundwater discharge to drains has decreased such that flows in 2012 were approximately 32,400 acre-ft less than the 1997–2000 average flow. This decrease was concentrated in the northern and southeastern parts of the subbasin, which corresponds with the areas of greatest groundwater pumping. Model simulation results of the Tule Lake subbasin groundwater model indicate that increased supplemental pumping is the dominant stress to the groundwater system in the subbasin. Simulated supplemental pumping and decreased recharge from irrigation between 2000 and 2010 totaled 323,573 acre-ft, 234,800 acre-ft (73 percent) of which was from supplemental pumping. The response of the groundwater system to this change in stress included about 180,500 acre-ft (56 percent) of decreased groundwater discharge to drains and a 126,000 acre-ft (39 percent) reduction in aquifer storage. The remaining 5 percent came from reduced groundwater flow to other model boundaries, including the Lost River, the Tule Lake sumps, and interbasin flow.

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 salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper

Aquatic Toxicology (Elsevier) | April 4th, 2016

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenil

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50 μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20 μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.

Effects of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 28th, 2018

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS BiOps, a study of the effects of the three SDABs (i.e., ORTB, MRB, and GLCB) on emigrating (i.e., out-migrating) juvenile salmonids was conducted (2010–2011) and the results are reported in this document. There were four effects considered in this study: 1) survival of juvenile salmonids (Ŝ); 2) juvenile salmonid time-in-vicinity (TIV) of a barrier; 3) predation on juvenile salmonids; and 4) predatory fish density evaluations near the barriers before-, during-, and after- construction during each study year. For one barrier, the ORTB, two-dimensional (2D) acoustic fish tracks for juvenile salmonids were used to evaluate: 1) the rates of successful passage through the barrier; and 2) route selection through the barrier. In addition, utilizing the ORTB 2D fish tracks for both juvenile salmonids and predatory fish, a mixture model (Romine et al. 2014) approach was employed to determine the probability that a juvenile salmonid had been eaten by a predatory fish in the vicinity of the ORTB.

Effects of Tidal Wetland Restoration on Fish: A Suite of Conceptual Models

California Department of Water Resources (DWR) | November 2nd, 2017

Fishes native to the Sacramento-San Joaquin Delta and Suisun Marsh have historically had access to a complex mosaic of dendritic channels, large tule marshes, floodplain

Fishes native to the Sacramento-San Joaquin Delta and Suisun Marsh have historically had access to a complex mosaic of dendritic channels, large tule marshes, floodplains, and riparian woodlands. After the Gold Rush, that habitat was rapidly and drastically altered, and today several native fish species occur in record low numbers. Although many other stressors also contributed to population declines, habitat restoration is a major component of strategies to reverse the trend. Programs such as the Fish Restoration Program particularly emphasize restoration of tidal wetlands and associated shallow subtidal habitat and strive to restore and learn in an adaptive management context. Conceptual models, therefore, are necessary to plan both the restoration and the monitoring and evaluation of restoration actions.