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 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 level observations in 250,000 coastal US wells reveal scope of potential seawater intrusion

Nature Portfolio (Springer Nature) | June 26th, 2020

Seawater intrusion into coastal aquifers can increase groundwater salinity beyond potable levels, endangering access to freshwater for millions of people. Seawater intrus

Seawater intrusion into coastal aquifers can increase groundwater salinity beyond potable levels, endangering access to freshwater for millions of people. Seawater intrusion is particularly likely where water tables lie below sea level, but can also arise from groundwater pumping in some coastal aquifers with water tables above sea level. Nevertheless, no nation-wide, observation-based assessment of the scope of potential seawater intrusion exists. Here we compile and analyze ~250,000 coastal groundwater-level observations made since the year 2000 in the contiguous United States. We show that the majority of observed groundwater levels lie below sea level along more than 15% of the contiguous coastline. We conclude that landward hydraulic gradients characterize a substantial fraction of the East Coast (>18%) and Gulf Coast (>17%), and also parts of the West Coast where groundwater pumping is high. Sea level rise, coastal land subsidence, and increasing water demands will exacerbate the threat of seawater intrusion.

Groundwater microbiomes balance resilience and vulnerability to hydroclimatic extremes

Nature Portfolio (Springer Nature) | August 20th, 2025

Groundwater Monitoring Protocols for Seawater Intrusion: Example of Challenges and Experiences in a Coastal Groundwater Basin

Groundwater Resources Association of California (GRA) | October 2nd, 2017

“Seawater intrusion refers to the advancement of seawater into a groundwater supply that results in degradation of water quality in the basin, and includes seawater fro

“Seawater intrusion refers to the advancement of seawater into a groundwater supply that results in degradation of water quality in the basin, and includes seawater from any source.” –GSP Emergency Regulations (Preface to a presentation by Kathleen Kuepper of the United Water Conservation District to the 26th annual meeting of the Groundwater Resources Association of California)

Groundwater Quality Data for the Madera/Chowchilla–Kings Shallow Aquifer Study Unit, 2013–14: Results from the California GAMA Program

U.S. Geological Survey (USGS) | February 2nd, 2017

Groundwater quality in the 2,390-square-mile Madera/Chowchilla–Kings Shallow Aquifer study unit was investigated by the U.S. Geological Survey from August 2013 to April

Groundwater quality in the 2,390-square-mile Madera/Chowchilla–Kings Shallow Aquifer study unit was investigated by the U.S. Geological Survey from August 2013 to April 2014 as part of the California State Water Resources Control Board Groundwater Ambient Monitoring and Assessment Program’s Priority Basin Project. The study was designed to provide a statistically unbiased, spatially distributed assessment of untreated groundwater quality in the shallow aquifer systems of the Madera, Chowchilla, and Kings subbasins of the San Joaquin Valley groundwater basin. The shallow aquifer system corresponds to the part of the aquifer system generally used by domestic wells and is shallower than the part of the aquifer system generally used by public-supply wells. This report presents the data collected for the study and a brief preliminary description of the results. Groundwater samples were collected from 77 wells and were analyzed for organic constituents, inorganic constituents, selected isotopic and age-dating tracers, and microbial indicators. Most of the wells sampled for this study were private domestic wells. Unlike groundwater from public-supply wells, the groundwater from private domestic wells is not regulated for quality in California and is rarely analyzed for water-quality constituents. To provide context for the sampling results, however, concentrations of constituents measured in the untreated groundwater were compared with regulatory and non-regulatory benchmarks established for drinking-water quality by the U.S. Environmental Protection Agency, the State of California, and the U.S. Geological Survey. Of the 319 organic constituents assessed in this study (90 volatile organic compounds and 229 pesticides and pesticide degradates), 17 volatile organic compounds and 23 pesticides and pesticide degradates were detected in groundwater samples; concentrations of all but 2 were less than the respective benchmarks. The fumigants 1,2-dibromo-3-chloropropane (DBCP) and 1,2-dibromoethane (EDB) were detected at concentrations above their respective regulatory benchmarks in samples from a total of four wells. Most detections of inorganic constituents were at concentrations or activities less than the respective benchmark levels. Five inorganic constituents were detected in groundwater samples from one or more wells at concentrations or activities greater than their respective regulatory, health-based benchmarks: arsenic, uranium, nitrate, adjusted gross alpha particle activity, and gross beta particle activity. Four inorganic constituents were detected in samples from one or more wells at concentrations or activities greater than their respective non-regulatory, health-based benchmarks: manganese, molybdenum, vanadium, and radon-222. Three inorganic constituents were detected in groundwater samples from one or more wells at concentrations greater than their respective non-regulatory, aesthetic-based benchmarks: iron, sulfate, and total dissolved solids. Microbial indicators (Escherichia coli, total coliform, and enterococci) were analyzed for presence or absence. The presence of Escherichia coli (E. coli) was not detected; the presence of total coliform was detected in samples from 10 of the 72 grid wells for which it was analyzed, and the presence of enterococci was detected in samples from 5 of the 73 grid wells analyzed.

Groundwater Quality Data for the Tahoe–Martis Study Unit, 2007: Results from the California GAMA Program

U.S. Geological Survey (USGS) | November 30th, 2007

Groundwater quality in the approximately 460-square-mile Tahoe–Martis study unit was investigated in June through September 2007 as part of the Priority Basin Project o

Groundwater quality in the approximately 460-square-mile Tahoe–Martis study unit was investigated in June through September 2007 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project was developed in response to the Groundwater Quality Monitoring Act of 2001 and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB).

Groundwater quality data in the Mojave study unit, 2008: Results from the California GAMA Program

U.S. Geological Survey (USGS) | July 1st, 2009

Groundwater Quality in Coachella Valley, California

U.S. Geological Survey (USGS) | January 9th, 2013

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monito

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The Priority Basin Project of the GAMA Program provides a comprehensive assessment of the State’s groundwater quality and increases public access to groundwater-quality information. Coachella Valley is one of the study areas being evaluated. The Coachella study area is approximately 820 square miles (2,124 square kilometers) and includes the Coachella Valley groundwater basin (California Department of Water Resources, 2003). Coachella Valley has an arid climate, with average annual rainfall of about 6 inches (15 centimeters). The runoff from the surrounding mountains drains to rivers that flow east and south out of the study area to the Salton Sea. Land use in the study area is approximately 67 percent (%) natural, 21% agricultural, and 12% urban. The primary natural land cover is shrubland. The largest urban areas are the cities of Indio and Palm Springs (2010 populations of 76,000 and 44,000, respectively). Groundwater in this basin is used for public and domestic water supply and for irrigation. The main water-bearing units are gravel, sand, silt, and clay derived from surrounding mountains. The primary aquifers in Coachella Valley are defined as those parts of the aquifers corresponding to the perforated intervals of wells listed in the California Department of Public Health database. Public-supply wells in Coachella Valley are completed to depths between 490 and 900 feet (149 to 274 meters), consist of solid casing from the land surface to a depth of 260 to 510 feet (79 to 155 meters), and are screened or perforated below the solid casing. Recharge to the groundwater system is primarily runoff from the surrounding mountains, and by direct infiltration of irrigation. The primary sources of discharge are pumping wells, evapotranspiration, and underflow to the Salton Sea and Imperial Valley areas.