San Joaquin River

Groundwater Conditions Report Water Year 2021

California Department of Water Resources (DWR) | March 15th, 2022

Groundwater Contributions of Flow, Nitrate, and Dissolved Organic Carbon to the Lower San Joaquin River, California, 2006–08

U.S. Geological Survey (USGS) | October 8th, 2013

The influence of groundwater on surface-water quality in the San Joaquin River, California, was examined for a 59-mile reach from the confluence with Salt Slough to Verna

The influence of groundwater on surface-water quality in the San Joaquin River, California, was examined for a 59-mile reach from the confluence with Salt Slough to Vernalis. The primary objective of this study was to quantify the rate of groundwater discharged to the lower San Joaquin River and the contribution of nitrate and dissolved organic carbon concentrations to the river. Multiple lines of evidence from four independent approaches were used to characterize groundwater contributions of nitrogen and dissolved organic carbon. Monitoring wells (in-stream and bank wells), streambed synoptic surveys (stream water and shallow groundwater), longitudinal profile surveys by boat (continuous water-quality parameters in the stream), and modeling (MODFLOW and VS2DH) provided a combination of temporal, spatial, quantitative, and qualitative evidence of groundwater contributions to the river and the associated quality. Monitoring wells in nested clusters in the streambed (in-stream wells) and on both banks (bank wells) along the river were monitored monthly from September 2006 to January 2009. Nitrate concentrations in the bank wells ranged from less than detection—that is, less than 0.01 milligrams per liter (mg/L) as nitrogen (N)—to approximately 13 mg/L as N. Nitrate was not detected at 17 of 26 monitoring wells during the study period. Dissolved organic carbon concentrations among monitoring wells were highly variable, but they generally ranged from 1 to 4 mg/L. In a previous study, 14 bank wells were sampled once in 1988 following their original installation. With few exceptions, specific conductivity and nitrate concentrations measured in this study were virtually identical to those measured 20 years ago. Streambed synoptic measurements were made by using a temporarily installed drive-point piezometer at 113 distinct transects across the stream during 4 sampling events. Nitrate concentrations exceeded the detection limit of 0.01 mg/L as N in 5 percent of groundwater samples collected from the in-stream wells as part of the synoptic surveys. Only 7 of the 113 cross-sectional transects had nitrate concentrations greater than 1 mg/L as N. In contrast, surface waters in the San Joaquin River tended to have nitrate concentrations in the 1–3 mg/L as N range. A zone of lower oxygen (less than 2 mg/L) in the streambed could limit nitrate contributions from regional groundwater flow because nitrate can be converted to nitrogen gas within this zone. Appreciable concentrations of ammonium (average concentration was 1.92 mg/L as N, and 95th percentile was 10.34 mg/L as N) in the shallow groundwater, believed to originate from anoxic mineralization of streambed sediments, could contribute nitrogen to the overlying stream as nitrate following in-stream nitrification, however. Dissolved organic carbon concentrations were highly variable in the shallow groundwater below the river (1 to 6 ft below streambed) and generally ranged between 1 and 5 mg/L, but had maximum concentrations in the 15–25 mg/L range. The longitudinal profile surveys were not particularly useful in identifying groundwater discharge areas. However, the longitudinal approach described in this report was useful as a baseline survey of measured water-quality parameters and for identifying tributary inflows that affect surface-water concentrations of nitrate. Results of the calibrated MODFLOW model indicated that the simulated groundwater discharge rate was approximately 1.0 cubic foot per second per mile (cfs/mi), and the predominant horizontal groundwater flow direction between the deep bank wells was westward beneath the river. The modeled (VS2DH) flux values (river gain versus river loss) were calculated for the irrigation and non-irrigation season, and these fluxes were an order of magnitude less than those from MODFLOW. During the irrigation season, the average river gain was 0.11 cfs/mi, and the average river loss was ?0.05 cfs/mi. During the non-irrigation season, the average river gain was 0.10 cfs/mi, and the average river loss was 0.08 cfs/mi.

Groundwater Data for Selected Wells Within the Eastern San Joaquin Groundwater Subbasin, California, 2003–8

U.S. Geological Survey (USGS) | June 1st, 2012

Data were collected by the U.S. Geological Survey from 2003 through 2008 in the Eastern San Joaquin Groundwater Subbasin, 80 miles east of San Francisco, California, as p

Data were collected by the U.S. Geological Survey from 2003 through 2008 in the Eastern San Joaquin Groundwater Subbasin, 80 miles east of San Francisco, California, as part of a study of the increasing chloride concentrations in groundwater processes. Data collected include geologic, geophysical, chemical, and hydrologic data collected during and after the installation of five multiple-well monitoring sites, from three existing multiple-well sites, and from 79 selected public-supply, irrigation, and domestic wells. Each multiple‑well monitoring site installed as part of this study contained three to five 2-inch diameter polyvinyl chloride (PVC)-cased wells ranging in depth from 68 to 880 feet below land surface. Continuous water-level data were collected from the 19 wells installed at these 5 sites and from 10 existing monitoring wells at 3 additional multiple-well sites in the study area. Thirty‑one electromagnetic logs were collected seasonally from the deepest PVC-cased monitoring well at seven multiple-well sites. About 200 water samples were collected from 79 wells in the study area. Coupled well‑bore flow data and depth-dependent water-quality data were collected from 12 production wells under pumped conditions, and well‑bore flow data were collected from 10 additional wells under unpumped conditions.

Groundwater depletion in California’s Central Valley accelerates during megadrought

Nature Portfolio (Springer Nature) | December 19th, 2022

Groundwater provides nearly half of irrigation water supply, and it enables resilience during drought, but in many regions of the world, it remains poorly, if at all mana

Groundwater provides nearly half of irrigation water supply, and it enables resilience during drought, but in many regions of the world, it remains poorly, if at all managed. In heavily agricultural regions like California’s Central Valley, where groundwater management is being slowly implemented over a 27-year period that began in 2015, groundwater provides two–thirds or more of irrigation water during drought, which has led to falling water tables, drying wells, subsiding land, and its long-term disappearance. Here we use nearly two decades of observations from NASA’s GRACE satellite missions and show that the rate of groundwater depletion in the Central Valley has been accelerating since 2003 (1.86 km3/yr, 1961–2021; 2.41 km3/yr, 2003–2021; 8.58 km3/yr, 2019–2021), a period of megadrought in southwestern North America. Results suggest the need for expedited implementation of groundwater management in the Central Valley to ensure its availability during the increasingly intense droughts of the future.

Groundwater Depletion in the United States (1900-2008)

U.S. Geological Survey (USGS) | June 1st, 2013

A natural consequence of groundwater withdrawals is the removal of water from subsurface storage, but the overall rates and magnitude of groundwater depletion in the Unit

A natural consequence of groundwater withdrawals is the removal of water from subsurface storage, but the overall rates and magnitude of groundwater depletion in the United States are not well characterized. This study evaluates long-term cumulative depletion volumes in 40 separate aquifers or areas and one land use category in the United States, bringing together information from the literature and from new analyses. Depletion is directly calculated using calibrated groundwater models, analytical approaches, or volumetric budget analyses for multiple aquifer systems. Estimated groundwater depletion in the United States during 1900–2008 totals approximately 1,000 cubic kilometers (km3). Furthermore, the rate of groundwater depletion has increased markedly since about 1950, with maximum rates occurring during the most recent period (2000–2008) when the depletion rate averaged almost 25 km3 per year (compared to 9.2 km3 per year averaged over the 1900–2008 time-frame). 

Groundwater development leads to decreasing arsenic concentrations in the San Joaquin Valley, California

Science of the Total Environment (Elsevier) | January 18th, 2021

In the San Joaquin Valley (SJV), California, about 10% of drinking water wells since 2010 had arsenic concentrations above the U.S. maximum contaminant level of 10μg/L.

In the San Joaquin Valley (SJV), California, about 10% of drinking water wells since 2010 had arsenic concentrations above the U.S. maximum contaminant level of 10μg/L. High concentrations of arsenic are often associated with high pH (greater than 7.8) or reduced geochemical conditions. Although most wells have low arsenic(<3μg/L) and do not have changing arsenic concentrations, this study found that most wells with concentrations above 10μg/L had arsenic trends. Overall, about 24% of wells had time-series trends since 2010 and 59% had paired-sample trends since 2000. Most wells had decreasing arsenic trends, even in wells with higher arsenic concentrations. These wells often had co-detections of increasing nitrate and sulfate trends that reflect oxic groundwater likely derived from agricultural recharge. Wells with increasing arsenic trends were deeper or located in the valley trough where aquifer materials are more fine-grained and where reducing conditions favor arsenic mobility. Wells with arsenic trends also tend to be clustered near areas of higher well density. Groundwater pumping in these areas has likely increased the contribution of younger, more oxic groundwater in wells with declining arsenic or, less frequently, increased the contribution of higher pH or reduced groundwater in wells with rising arsenic. Projections of arsenic trends indicate that 37 wells with high arsenic presently will be below 10μg/L in ten years. Unfortunately, these improvements will be largely offset by 31 wells that are expected to increase above 10μg/L in addition to expected rises in nitrate in wells where arsenic decreased. This study shows how human-altered flow systems can impact the natural geochemical character of water in both beneficial and deleterious ways.

Groundwater dominates snowmelt runoff and controls streamflow efficiency in the western United States

Nature Portfolio (Springer Nature) | May 3rd, 2025

Groundwater in California

Public Policy Institute of California (PPIC) | June 6th, 2024

Groundwater Management and Safe Drinking Water in the San Joaquin Valley

Water Foundation | June 2nd, 2020

Groundwater Management Principles and Strategies to Monitor, Analyze and Minimize Impacts to Drinking Water Wells: A Framework for State Action to Support Drought Resilient Communities

California Department of Water Resources (DWR) | December 15th, 2021

This framework was developed in response to support drinking water access for groundwater-dependent communities.

This framework was developed in response to support drinking water access for groundwater-dependent communities.