San Joaquin River

Environmental Baseline Biological Resources - Fauna, Total Water Management Study for the Central Valley, California

U.S. Bureau of Reclamation (USBR) | January 1st, 1975

Environmental Characteristics of Select Managed Ponds in the Sacramento–San Joaquin Delta: Implications for Native Fish Conservation and Research

U.S. Geological Survey (USGS) | July 23rd, 2025

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpos

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt (Hypomesus transpacificus). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass (Micropterus salmoides) and black crappie (Pomoxis nigromaculatus) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

Environmental Water Account: Need for Legislative Definition and Oversight

Legislative Analyst's Office (LAO) | January 29th, 2001

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered s

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered species protection and recovery in the Bay-Delta region. There are many policy and implementation issues that the Legislature should consider before CALFED proceeds with the new program, including the program's costs, benefits, impacts, governance, and funding. Funding should be governed by the "beneficiary pays" principle.

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river

Environmental Biology of Fishes (Springer) | June 6th, 2008

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and floodplain habitats. Fish were placed in enclosures during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon reared in floodplain and river enclosures. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation experienced higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the non-tidal river upstream of the floodplain varied with flow in the river. When flows were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish displayed very poor growth in tidally influenced river habitat below the floodplain, a habitat type to which juveniles are commonly displaced during high flow events due to a lack of channel complexity in the main-stem river. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river. Variable responses in both growth and mortality, however, indicate the importance of providing habitat complexity for juvenile salmon in floodplain reaches of streams, so fish can find optimal places for rearing under different flow conditions.

Escalating Hydrological Extremes and Whiplashes in the Western U.S.: Challenges for Water Management and Frontline Communities

American Geophysical Union (AGU) | May 14th, 2025

Estimates of Natural and Unimpaired Flows for the Central Valley of California: Water Years 1922-2014 (draft)

California Department of Water Resources (DWR) | March 1st, 2016

Estimating regional water supplies that would have occurred absent human activities is a common practice in water resources planning. In this report, such theor

Estimating regional water supplies that would have occurred absent human activities is a common practice in water resources planning. In this report, such theoretical water supply estimates are referred to as “unimpaired” flow. Since 1980, the Department of Water Resources (Department) has periodically published estimates of Central Valley unimpaired flows. In spite of the Department’s previous attempts to distinguish between natural conditions and its calcula tion of theoretical unimpaired flows, unimpaired flow estimates have frequently been used as a surrogate measure of natural conditions, presumably because natural flow estimates were unavailable. A major objective of this report is to clarify the conceptua l differences between natural and unimpaired flows. In this report, the term “unimpaired” flow is used to describe a theoretically available water supply assuming existing river channel conditions in the absence of (1) storage regulation for water supply a nd hydropower purposes and (2) stream diversions for agricultural and municipal uses. Unimpaired flow estimates are theoretical in that such conditions have not occurred historically. In pristine watersheds which have undergone little land use change, unim paired flow estimates provide a fixed frame of reference to develop relationships between precipitation, runoff, and water supply based on long - term hydrologic records. For many years these relationships were based on the assumption of stationarity, i.e. that the past is a good indicator of the future. However, global warming now requires hydrologists and water resources managers to analyze non-stationary processes, requiring more sophisticated tools and techniques to quantify future water supplies. This report updates and extends the Department’s previous published estimates of unimpaired flows for 24 Central Valley sub-basins and the Delta. Monthly unimpaired flows are presented for water years 1922 - 2014.

Estimating the permanent loss of groundwater storage in the southern San Joaquin Valley, California

American Geophysical Union (AGU) | February 23rd, 2017

In the San Joaquin Valley, California, recent droughts starting in 2007 have increased the pumping of groundwater, leading to widespread subsidence. In the southern porti

In the San Joaquin Valley, California, recent droughts starting in 2007 have increased the pumping of groundwater, leading to widespread subsidence. In the southern portion of the San Joaquin Valley, vertical subsidence as high as 85 cm has been observed between June 2007 and December 2010 using Interferometric Synthetic Aperture Radar (InSAR). This study seeks to map regions where inelastic (not recoverable) deformation occurred during the study period, resulting in permanent compaction and loss of groundwater storage. We estimated the amount of permanent compaction by incorporating multiple data sets: the total deformation derived from InSAR, estimated skeletal-specific storage and hydraulic parameters, geologic information, and measured water levels during our study period. We used two approaches, one that we consider to provide an estimate of the lowest possible amount of inelastic deformation, and one that provides a more reasonable estimate. These two approaches resulted in a spatial distribution of values for the percentage of the total deformation that was inelastic, with the former estimating a spatially averaged value of 54%, and the latter a spatially averaged value of 98%. The former corresponds to the permanent loss of m3 of groundwater storage, or roughly 5% of the volume of groundwater used over the study time period; the latter corresponds to the loss of m3 of groundwater storage, or roughly 9% of the volume of groundwater used. This study demonstrates that a data-driven approach can be used effectively to estimate the permanent loss of groundwater storage.

Estimation of groundwater residence time with deeply-derived carbon mixture considered in California

Science of the Total Environment (Elsevier) | December 16th, 2022

Groundwater has experienced long-term overdraft due to drought and human activities in California, resulting in issues of land subsidence and groundwater anthropogenic co

Groundwater has experienced long-term overdraft due to drought and human activities in California, resulting in issues of land subsidence and groundwater anthropogenic contamination. As a useful indicator of groundwater renewal rate and its residence time, groundwater age has been conventionally investigated based on 14C content and 3H concentration. However, the influence of deeply-derived (endogenic) CO2 mixture is not fully and quantitatively considered, although endogenic carbon contributes a large part of the dissolved inorganic carbon in groundwater. Combined with 3H concentration, both conventional and modified 14C-dating methods with endogenic CO2 mixture considered are employed for groundwater age determination in California. On average, the conventional groundwater 14C apparent age is overestimated by ~4.9 kyr or ~26.2 %, causing groundwater recharge rate underestimation and aquifer recovery time overestimation by ~46.0 % and ~26.2 %, respectively. High 3H concentration indicates modern water mixture in more than one fifth of groundwater samples, including those with high modified 14C apparent age (> 12 kyr, i.e., fossil groundwater) in the Central Valley and southern California, which are generally considered not to be recharged by modern water. Modern water mixture in old groundwater can potentially bring anthropogenic contamination to these groundwater resources, which should be paid attentions by the government and the managers. The results have important implications in evaluation of groundwater replenishment and its susceptibility to modern contamination in California, and in groundwater resources estimation globally.

Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)

University of California, Davis (UC Davis) | December 1st, 2020

White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance because of a variety of factors. The purpose o

White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance because of a variety of factors. The purpose of our study was to identify the estuarine habitat used by White Sturgeon to aid in the conservation and management of the species locally and across its range. We seasonally sampled sub-adult and adult White Sturgeon in the central estuary using setlines across a habitat gradient representative of three primary structural elements: shallow wetland channel (mean sample depth = 2 m), shallow open-water shoal (mean sample depth = 2 m), and deep open-water channel (mean sample depth = 7 m). We found that the shallow open-water shoal and deep open-water channel habitats were consistently occupied by White Sturgeon in spring, summer, and fall across highly variable water quality conditions, whereas the shallow wetland channel habitat was essentially unoccupied. We conclude that sub-adult and adult White Sturgeon inhabit estuaries in at least spring, summer, and fall and that small, shallow wetland channels are relatively unoccupied.

Estuary News, April 1993

Publisher not available | April 15th, 1993