San Joaquin River

Juvenile Production Estimate (JPE) Calculation and Use/Application of Survival Data from Acoustically-tagged Chinook Salmon Releases Report

Delta Stewardship Council (Delta Council) | February 21st, 2014

Each year, NOAA’s National Marine Fisheries Service (NMFS) estimates the number of juvenile winter-run Chinook salmon expected to enter the Delta. NMFS’ June 4, 2009

Each year, NOAA’s National Marine Fisheries Service (NMFS) estimates the number of juvenile winter-run Chinook salmon expected to enter the Delta. NMFS’ June 4, 2009, biological and conference opinion on the long-term operation of the Central Valley Project and State Water Project provides an incidental take limit on natural juvenile winter-run based on the juvenile production estimate.

Klamath/San Joaquin/Sacramento Hydroclimatic Reconstructions from Tree Rings

California Department of Water Resources (DWR) | February 7th, 2014

This is a draft final report for Agreement Number 4600008850, “Klamath/San Joaquin/Sacramento Hydroclimatic Reconstructions”, signed October 13, 2010.  Work includes

This is a draft final report for Agreement Number 4600008850, “Klamath/San Joaquin/Sacramento Hydroclimatic Reconstructions”, signed October 13, 2010.  Work includes developing new and updated tree-ring chronologies, reconstructing specified streamflow and/or precipitation records in the Klamath, San Joaquin and Sacramento River Basins, and analyzing the time series properties of the reconstructions. These reconstructions allow assessment of hydrologic variability over centuries to millennia and give context for assessing recent drought events. Tasks on this project included field collections; laboratory work in sample preparation, dating and measurement; and statistical work in chronology development, reconstruction, and analysis of those reconstructions. The interpretation of the reconstructions includes five main components : 1) place instrumental-period flow statistics in a long-term context, 2) quantify droughts and wet periods, 3) identify cycles in wetness and dryness, 4) check consistency with other paleoclimatic data, and 5) assess reconstructed flow variations in the context of expected scenarios of climate. A total of 16 different hydroclimatic series – 11 flow records and 5 precipitation records, were reconstructed. This report summarizes the research project products and results. The Data and Methods section of this report describes the field collections and development of tree-ring chronologies, reconstruction modeling, and methods of analyzing reconstructions. The Results section focuses on the interpretation of selected key reconstructions for the Klamath, Sacramento, and San Joaquin basins. Annual time series of the 16 reconstructions are included as products in an appendix and in a digital spreadsheet.

Land Reclamation Impacts on Tidal Landscape Evolution

American Geophysical Union (AGU) | August 21st, 2025

Fertile and low-lying coastal landscapes are often densely populated due to food supply (agriculture, aquaculture, and fisheries) and easy navigability (shipping lanes).

Fertile and low-lying coastal landscapes are often densely populated due to food supply (agriculture, aquaculture, and fisheries) and easy navigability (shipping lanes). Much of the low-lying land that is regularly inundated by the sea has been converted to agricultural land or urban environments to meet the need for land. This reclamation of land influences the tidal dynamics of the coastal environment, which in turn modifies its morphology. Through various complex tide-topography interactions identified in this paper, we explore how the location and extent of land reclamation influences tides and bed levels in various tidal environments. We especially point to the key role of sediments herein, introducing feedback mechanisms that lead to large impacts on tidal landscapes, but also long adaptation times. This is especially the case for estuaries due to their confinement and the typically large availability of sediments.

Land subsidence along the California Aqueduct in west-central San Joaquin Valley, California, 2003–10

U.S. Geological Survey (USGS) | November 29th, 2018

Extensive groundwater withdrawal from the unconsolidated deposits in the San Joaquin Valley caused widespread aquifer-system compaction and resultant land subside

Extensive groundwater withdrawal from the unconsolidated deposits in the San Joaquin Valley caused widespread aquifer-system compaction and resultant land subsidence from 1926 to 1970—locally exceeding 8.5 meters. The importation of surface water beginning in the early 1950s through the Delta-Mendota Canal and in the early 1970s through the California Aqueduct resulted in decreased groundwater pumping, recovery of water levels, and a reduced rate of compaction in some areas of the San Joaquin Valley. However, drought conditions during 1976–77, 1987–92, and drought conditions and operational reductions in surface-water deliveries during 2007–10 decreased surface-water availability, causing pumping to increase, water levels to decline, and renewed compaction. Land subsidence from this compaction has reduced freeboard and flow capacity of the California Aqueduct, Delta-Mendota Canal, and other canals that deliver irrigation water and transport floodwater. The U.S. Geological Survey, in cooperation with the California Department of Water Resources, assessed more recent land subsidence near a 145-kilometer reach of the California Aqueduct in the west-central part of the San Joaquin Valley as part of an effort to minimize future subsidence-related damages to the California Aqueduct. The location, magnitude, and stress regime of land-surface deformation during 2003–10 were determined by using data and analyses associated with extensometers, Global Positioning System surveys, Interferometric Synthetic Aperture Radar, spirit-leveling surveys, and groundwater wells. Comparison of continuous Global Positioning System, shallow-extensometer, and groundwater-level data indicated that most of the compaction in this area took place beneath the Corcoran Clay, the primary regional confining unit. The integration of measurements strengthens confidence in individual measurement methods and provides the information at spatial and temporal scales that water managers need to design and implement groundwater sustainability plans in compliance with California’s Sustainable Groundwater Management Act. Measurements of land-surface deformation during 2003–10 indicated that the parts of the California Aqueduct closest to the Coast Ranges in the west-central part of the San Joaquin Valley were fairly stable or minimally subsiding on an annual basis; some areas show seasonal periods of subsidence and uplift that resulted in little or no longer-term elevation loss. Many groundwater levels in these areas did not reach historical lows during 2003–10, indicating that deformation nearest the Coast Ranges was likely primarily elastic. Land-surface deformation measurements indicated that some parts of the California Aqueduct that traverse farther from the Coast Ranges toward the valley center subsided. Some parts of the California Aqueduct subsided locally, but generally the California Aqueduct is within part of a 12,000-square-kilometer area affected by 25 millimeters or more of subsidence during 2008–10, with maxima in Madera County, south of the town of El Nido near the San Joaquin River and the Eastside Bypass (540 millimeters), and in Tulare County, west of the town of Pixley (345 millimeters). Interferometric Synthetic Aperture Radar-derived subsidence maps for various periods during 2003–10 show that the area of maximum active subsidence (that is, the largest rates of subsidence) shifted from its historical (1926–70) location southwest of the town of Mendota to these areas nearer the valley center. Calculations indicated that the subsidence rate doubled in 2008 in parts of the study area. Water levels declined during 2007–10 in many shallow and deep wells in the most rapidly subsiding areas, where water levels in many deep wells reached their historical lows, indicating that subsidence measured during this period was largely inelastic. Continued groundwater-level and land-subsidence monitoring in the San Joaquin Valley is important because (1) operational- and drought-related reductions in surface-water deliveries since 1976 have resulted in increased groundwater pumping and associated water-level declines and land subsidence, (2) land use and associated pumping continue to change throughout the valley, and (3) subsidence management is stipulated in the Sustainable Groundwater Management Act. The availability of surface water remains uncertain; even during record-setting precipitation years, such as 2010–11, water deliveries fell short of requests and groundwater pumping was required to meet the irrigation demand. In some areas, the infrastructure is not available to supply surface water, and groundwater is the only source of water. Because of the expected continued demand for water and the limitations and uncertainty of surface-water supplies, groundwater pumping and associated land subsidence remains a concern. Spatially detailed information on land subsidence is needed to minimize future subsidence-related damages to the California Aqueduct and other infrastructure in the San Joaquin Valley, as well as alterations to natural resources such as stream gradients, water depths, and water temperatures. The integration of data on land-surface elevation, subsurface deformation, and water levels—particularly continuous measurements—enables the analysis of aquifer-system response to groundwater pumping, which in turn, enables estimation of the preconsolidation head and calculation of aquifer-system storage properties. This information can be used to improve numerical model simulations of groundwater flow and aquifer-system compaction and allow for consideration of land subsidence in the evaluation of water resource management alternatives and compliance with the Sustainable Groundwater Management Act.

Land Subsidence along the Delta-Mendota Canal in the Northern Part of the San Joaquin Valley, California, 2003–10

U.S. Geological Survey (USGS) | November 19th, 2013

Extensive groundwater withdrawal from the unconsolidated deposits in the San Joaquin Valley caused widespread aquifer-system compaction and resultant land subsidence from

Extensive groundwater withdrawal from the unconsolidated deposits in the San Joaquin Valley caused widespread aquifer-system compaction and resultant land subsidence from 1926 to 1970—locally exceeding 8.5 meters. The importation of surface water beginning in the early 1950s through the Delta-Mendota Canal and in the early 1970s through the California Aqueduct resulted in decreased pumping, initiation of water-level recovery, and a reduced rate of compaction in some areas of the San Joaquin Valley. However, drought conditions during 1976–77 and 1987–92, and drought conditions and regulatory reductions in surface-water deliveries during 2007–10, decreased surface-water availability, causing pumping to increase, water levels to decline, and renewed compaction. Land subsidence from this compaction has reduced freeboard and flow capacity of the Delta-Mendota Canal, the California Aqueduct, and other canals that deliver irrigation water and transport floodwater. The U.S. Geological Survey, in cooperation with the U.S. Bureau of Reclamation and the San Luis and Delta-Mendota Water Authority, assessed land subsidence in the vicinity of the Delta-Mendota Canal as part of an effort to minimize future subsidence-related damages to the canal. The location, magnitude, and stress regime of land-surface deformation during 2003–10 were determined by using extensometer, Global Positioning System (GPS), Interferometric Synthetic Aperture Radar (InSAR), spirit leveling, and groundwater-level data. Comparison of continuous GPS, shallow extensometer, and groundwater-level data, combined with results from a one-dimensional model, indicated the vast majority of the compaction took place beneath the Corcoran Clay, the primary regional confining unit. Land-surface deformation measurements indicated that much of the northern portion of the Delta-Mendota Canal (Clifton Court Forebay to Check 14) was fairly stable or minimally subsiding on an annual basis; some areas showed seasonal periods of subsidence and of uplift that resulted in little or no longer-term elevation loss. Many groundwater levels in this northern area did not reach historical lows during 2003–10, indicating that deformation in this region was primarily elastic. Although the northern portion of the Delta-Mendota Canal was relatively stable, land-surface deformation measurements indicated the southern portion of the Delta-Mendota Canal (Checks 15–21) subsided as part of a large subsidence feature centered about 15 kilometers northeast of the Delta-Mendota Canal, south of the town of El Nido. Results of InSAR analysis indicated at least 540 millimeters of subsidence near the San Joaquin River and the Eastside Bypass during 2008–10, which is part of a 3,200 square-kilometer area—including the southern part of the Delta-Mendota Canal—affected by 20 millimeters or more of subsidence during the same period. Calculations indicated that the subsidence rate doubled in 2008 in some areas. The GPS surveys done in 2008 and 2010 confirmed the high subsidence rate measured by using InSAR for the same period. Water levels in many shallow and deep wells in this area declined during 2007–10; water levels in many deep wells reached historical lows, indicating that subsidence measured during this period was largely inelastic. InSAR-derived subsidence maps for various periods during 2003–10 showed that the area of maximum active subsidence (that is, the largest rates of subsidence) shifted from its historical (1926–70) location southwest of Mendota to south of El Nido. Continued groundwater-level and land-subsidence monitoring in the San Joaquin Valley is important because (1) regulatory- and drought-related reductions in surface-water deliveries since 1976 have resulted in increased groundwater pumping and associated land subsidence, and (2) land use and associated groundwater pumping continue to change throughout the valley. The availability of surface water remains uncertain; even during record-setting precipitation years, such as 2010–11, water deliveries have fallen short of requests and groundwater pumping was required to meet the irrigation demand. Due to the expected continued demand for irrigation supply water and the limitations and uncertainty of surface-water supplies, groundwater pumping and associated land subsidence is likely to continue in the future. Spatially detailed information on land subsidence is needed to facilitate minimization of future subsidence-related damages to the Delta-Mendota Canal and other infrastructure in the San Joaquin Valley. The integration of subsidence, deformation, and water-level measurements—particularly continuous measurements—enables the analysis of aquifer-system response to increased groundwater pumping, which in turn, enables identification of the preconsolidation head and calculation of aquifer-system storage properties. This information can be used to improve numerical model simulations of groundwater flow and aquifer-system compaction and allow for consideration of land subsidence in the evaluation of water-resource management alternatives.

Land subsidence in the San Joaquin Valley, California, as of 1972

U.S. Geological Survey (USGS) | July 10th, 1975

Land subsidence which began in the mid-1920's due to groundwater overdraft in the San Joaquin Valley has caused widespread concern for the past two decades. Withdrawals

Land subsidence which began in the mid-1920's due to groundwater overdraft in the San Joaquin Valley has caused widespread concern for the past two decades. Withdrawals for irrigation increased from 3 million acre-feet in 1942 to 10 million acre-feet in 1966. Water levels declined at unprecedented rates during the 1950's and early 1960's. Pumping lifts became inordinately high, well casings failed at alarming rates, and differential settlement caused numerous farming and engineering problems. By 1970,5,200 square miles of valley land had been affected, and maximum subsidence exceeded 28 feet. The valley-wide volume of subsidence totaled 15.6 million acre-feet, one-half the initial storage capacity of Lake Mead. This subsidence represents one of the great environmental changes imposed by man. Importation of surface water to the northwestern and eastern areas of overdraft in the valley began in the 1950's and to the much larger western and southern areas in the late 1960's. Canal imports have largely replaced ground-water pumpage in these areas. As of 1973, after three decades of continued declining water levels, many hundreds of irrigation wells are idle and water levels are rising. Throughout much of the valley, artesian pressures are recovering toward their presubsidence levels, and elevations of the subsiding land surface are stabilizing. Basic-data graphs and computer-plotted stress-strain relationships constitute a major part of this report. They are based on 10-13 years of detailed field measurements of both water-level change and compaction collected by the U.S. Geological Survey at 20 selected locations in the San Joaquin Valley. The recharge characteristics of a ground-water reservoir are indicated roughly by the volume ratio, which is subsidence/pumpage. In the Los Banos-Kettleman City area, the values of this ratio range from less than 0.2 near the perimeter to more than 0.6 in the central part of the area. In the corresponding parts of the Arvin-Maricopa area, the ratio ranges from near 0 to more than 0.4.

Land subsidence in the San Joaquin Valley, California, as of 1980

U.S. Geological Survey (USGS) | July 1st, 1984

Land subsidence in the San Joaquin Valley, California, USA, 2007–2014

Copernicus Publications | November 12th, 2015

Land Transitions and Dust in the San Joaquin Valley

Public Policy Institute of California (PPIC) | July 24th, 2022

The Sustainable Groundwater Management Act (SGMA) requires groundwater users to bring their basins into balance over the next two decades. In the San Joaquin Valley, this

The Sustainable Groundwater Management Act (SGMA) requires groundwater users to bring their basins into balance over the next two decades. In the San Joaquin Valley, this will mean taking more than 500,000 acres of agricultural land out of intensive irrigated production. Among other issues, this could potentially lead to air quality impacts if the lands become new sources of dust, especially windblown dust, which can have numerous negative short- and long-term health and environmental impacts. In addition, the changing climate may exacerbate risks as warmer temperatures can dry out soils and increase dust emissions. The overall air quality impact of transitioning agricultural land to new uses is nuanced, but proactive management can help to identify high-risk areas and at-risk communities, and direct effort and funding to the most cost-effective interventions.

Land use and land cover influence on water quality in the last free-flowing river draining the western Sierra Nevada, California

Journal of Hydrology (Elsevier) | November 10th, 2005

Land use and land cover across 28 sub-basins within the Cosumnes Watershed, CA (1989 km2) were correlated to nitrate-N and total suspended solids (TSS) loading between w

Land use and land cover across 28 sub-basins within the Cosumnes Watershed, CA (1989 km2) were correlated to nitrate-N and total suspended solids (TSS) loading between water years 1999 and 2001. The impact of human development on stream water quality was evident as both agricultural area and population density predicted TSS loading in a linear mixed effects model. In contrast to the TSS model, the nitrate-N loading model was more complex with agriculture, grassland, and the presence or absence of waste water treatment plants (WWTPs) all contributing. The lack of correlation between population density and nitrate-N loading indicates that human habitation of the landscape does not impact stream nitrate levels until a WWTP is built within the sub-basin. During dry water years the models predict a linear reduction in TSS loading but the correlations to agriculture and population density remain positive. In contrast, nitrate is positively correlated to grasslands during average water years and negatively correlated during dry water years. Analysis of constituent fluxes from the upper watershed versus the lower watershed indicates that silica is derived primarily from the uplands and that during dry water years the upper watershed is an important source of dissolved organic carbon (DOC) and nitrate. The lower watershed contributes the majority of the sediment and nutrients during both dry and average water years, the one caveat being that during dry years the lower basin becomes a nitrate sink.