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Scientific Investigations Report 2009–5266

Prepared in cooperation with the California State Water Resources Control Board

Status and Understanding of Groundwater Quality in the Central–Eastside San Joaquin Basin, 2006: California GAMA Priority Basin Project

By Matthew K. Landon, Kenneth Belitz, Bryant C. Jurgens, Justin T. Kulongoski, and Tyler D. Johnson


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Groundwater quality in the approximately 1,695-square-mile Central Eastside San Joaquin Basin (Central Eastside) study unit was investigated as part of the Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA PBP was developed in response to the California Groundwater Quality Monitoring Act of 2001, and is being conducted by the California State Water Resources Control Board in collaboration with the U.S. Geological Survey and the Lawrence Livermore National Laboratory. The GAMA Central Eastside study unit was designed to provide a spatially unbiased assessment of untreated-groundwater quality, as well as a statistically consistent basis for comparing water quality throughout California. During March through June 2006, samples were collected from 78 wells in Stanislaus and Merced Counties, 58 of which were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study unit (grid wells), and 20 of which were sampled to evaluate changes in water chemistry along groundwater-flow paths (understanding wells). Water-quality data from the California Department of Public Health (CDPH) database also were used for the assessment.

An assessment of the current status of the groundwater quality included collecting samples from wells for analysis of anthropogenic constituents such as volatile organic compounds (VOCs) and pesticides, as well as naturally occurring constituents such as major ions and trace elements. The assessment of status is intended to characterize the quality of untreated-groundwater resources within the primary aquifer system, not the treated drinking water delivered to consumers by water purveyors. The primary aquifer system (hereinafter, primary aquifer) is defined as that part of the aquifer corresponding to the perforation interval of wells listed in the CDPH database for the Central Eastside study unit. The quality of groundwater in shallower or deeper water-bearing zones may differ from that in the primary aquifer; shallower groundwater may be more vulnerable to surficial contamination. The primary aquifer is represented by the grid wells, of which 90 percent had depths to the tops of their perforations of about 80 to 330 feet and depths to bottom of about 100 to 670 feet. Relative-concentrations (sample concentration divided by benchmark concentration) were used as the primary metric for assessing the status of water quality for those constituents that have Federal and (or) California human health or aesthetic benchmarks. A relative-concentration greater than (>) 1.0 indicates a concentration above a benchmark, and less than or equal to (≤) 1.0 indicates a concentration equal to or below a benchmark. For organic and special interest constituents, relative-concentrations were classified as high (>1.0), moderate (≤1.0 and >0.1), or low (≤0.1). For inorganic constituents, relative-concentrations were classified as high (>1.0), moderate (≤1.0 and >0.5), or low (≤0.5). The threshold between low and moderate classifications was lower for organic and special interest constituents than for inorganic constituents because organic constituents generally are less prevalent and have smaller relative-concentrations than inorganic constituents.

Grid-based and spatially-weighted approaches, the latter incorporating data from all CDPH wells, were used to evaluate the proportion of the primary aquifer (aquifer-scale proportions) with high, moderate, or low relative-concentrations. For individual constituents or classes of constituents, the aquifer-scale high proportion is the percentage of the area of the study unit having high relative-concentrations within the depth-zones of the primary aquifer. Aquifer-scale moderate and low proportions are defined similarly. Spatially-weighted aquifer-scale high proportions nearly always fell within the 90-percent confidence interval of grid-based aquifer-scale high proportions, indicating that the grid-based approach yielded statistically equivalent results to the spatially-weighted approach incorporating CDPH data.

The status assessment for inorganic constituents showed that inorganic constituents (one or more) were high, relative to human-health benchmarks, in 18.0 percent of the primary aquifer, moderate in 44.0 percent, and low in 38.0 percent. Of inorganic constituents with human-health benchmarks, arsenic, vanadium, and nitrate were detected at high relative-concentrations in 15.6 percent, 3.6 percent, and 2.1 percent, respectively, of the primary aquifer. Of inorganic constituents with secondary maximum contaminant levels (SMCL), manganese, iron, and TDS were detected at high relative-concentrations in 4.5 percent, 2.2 percent, and 1.7 percent, respectively, of the primary aquifer.

The status assessment for organic constituents showed that organic constituents (one or more) were high, relative to human-health benchmarks, in a smaller proportion of the primary aquifer (1.2 percent) than inorganic constituents (18.0 percent). Organic constituents had moderate relative-concentrations in 14.3 percent, and had low relative-concentrations or were not detected in 84.5 percent, of the primary aquifer. The proportion of the primary aquifer with high relative-concentrations of organic constituents reflected high proportions of the discontinued soil fumigant 1,2-dibromo-3-chlororopane (DBCP; 1.0 percent) and the solvent tetrachloroethene (PCE; 0.2 percent). Most of the organic and special interest constituents detected in groundwater in the Central Eastside study unit have human-health benchmarks. Of the 205 organic and special interest constituents analyzed for, 36 constituents were detected. Of these constituents, 32 were detected only at low relative-concentrations. Four constituents, chloroform, carbon tetrachloride, DBCP, and perchlorate, were detected at moderate relative-concentrations in grid wells. Nine organic and special-interest constituents were detected frequently (detected in greater than 10 percent of samples): the trihalomethanes chloroform, bromoform, bromodichloromethane, and dibromochloromethane; the solvent PCE; the herbicides atrazine, simazine, and metolachlor, and special-interest constituent perchlorate.

An assessment of understanding of the groundwater quality included sampling of understanding wells, some of which were perforated in shallower or deeper portions of the aquifer system than the primary aquifer, and analysis of correlations of groundwater quality with land use, depth, age classification, and other potential explanatory factors.

The understanding assessment indicated that the concentrations of many constituents were related to depth and groundwater age. However, concentrations of individual constituents or constituent classes also were sometimes related to geochemical conditions, lateral position in the flow system, or land use.

High and moderate relative-concentrations of uranium, nitrate, and total dissolved solids (TDS) were detected in some wells where the tops of perforations are within the upper 200 feet of the aquifer system. In wells with the depth to the top of perforations below this depth, concentrations were low. A similar pattern occurred for the sum of herbicide concentrations. These vertical water-chemistry patterns are consistent with the hydrogeologic setting, in which return flows from agricultural and urban land use are the major source of recharge, and withdrawals for irrigation and urban supply are the major source of discharge, resulting in substantial vertical components of groundwater flow.

The decrease in concentrations of many constituents with depth reflects in part that groundwater gets older with depth. Tritium, helium-isotopes, and carbon-14 data were used to classify the predominant age of groundwater samples into three categories: modern (water that has entered the aquifer in the last 50 years), pre-modern (water that entered the aquifer more than 50 years, up to tens of thousands of years, ago), and mixed (mixtures of waters with modern and pre-modern ages). Uranium, nitrate, and herbicide concentrations were significantly higher in groundwater having modern- and mixed-ages than pre-modern ages, indicating that these constituents may be affected by anthropogenic activities in the last 50 years.

Other patterns in the distribution of nitrate, uranium, and TDS are evident. Isotopic and geochemical data are consistent with partial denitrification of nitrate in some reducing groundwaters in the western and deeper parts of the flow system. Uranium and TDS concentrations increase from east to west across the valley, along the direction of regional lateral groundwater flow.

High and moderate relative-concentrations of arsenic can be attributed to reductive dissolution of manganese or iron oxides, or to desorption by high pH waters. Arsenic concentrations also increased with increasing depth and groundwater age. High to moderate relative-concentrations of vanadium primarily are related to high pH under oxic conditions.

The frequency of detections of DBCP was greater in areas with orchard-vineyard land use >40 percent and at depths <200 feet. THMs and solvents were correlated positively with percent urban land use. Herbicide concentrations were correlated negatively with percent natural land use. Perchlorate concentrations were significantly greater in waters having modern and mixed ages than waters having pre-modern ages and were significantly and positively correlated with two land uses—percent orchard/vineyard land use and percent urban land use.

First posted April 13, 2010

For additional information contact:
Director, California Water Science Center
U.S. Geological Survey
6000 J Street, Placer Hall
Sacramento, California 95819

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Suggested citation:

Landon, M.K., Belitz, Kenneth, Jurgens, B.C., Kulongoski, J.T., and Johnson, T.D., 2010, Status and understanding of groundwater quality in the Central–Eastside San Joaquin Basin, 2006: California GAMA Priority Basin project: U.S. Geological Survey Scientific Investigations Report 2009–5266, 97 p.




Purpose and Scope

Description of Study Unit


Attributes of Wells

Status and Understanding of Water Quality




Appendix A. Attributes of USGS–GAMA and CDPH Grid Wells

Appendix B. Comparison of CDPH and USGS–GAMA Data

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