Groundwater quality in the approximately 860-square-mile Madera and Chowchilla Subbasins (Madera-Chowchilla study unit) of the San Joaquin Valley Basin was investigated as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The study unit is located in California's Central Valley region in parts of Madera, Merced, and Fresno Counties. The GAMA Priority Basin Project is being conducted by the California State Water Resources Control Board in collaboration with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory. The Project was designed to provide statistically robust assessments of untreated groundwater quality within the primary aquifer systems in California. The primary aquifer system within each study unit is defined by the depth of the perforated or open intervals of the wells listed in the California Department of Public Health (CDPH) database of wells used for municipal and community drinking-water supply. The quality of groundwater in shallower or deeper water-bearing zones may differ from that in the primary aquifer system; shallower groundwater may be more vulnerable to contamination from the surface. The assessments for the Madera-Chowchilla study unit were based on water-quality and ancillary data collected by the USGS from 35 wells during April-May 2008 and water-quality data reported in the CDPH database. Two types of assessments were made: (1) status, assessment of the current quality of the groundwater resource, and (2) understanding, identification of natural factors and human activities affecting groundwater quality. The primary aquifer system is represented by the grid wells, of which 90 percent (%) had depths that ranged from about 200 to 800 feet (ft) below land surface and had depths to the top of perforations that ranged from about 140 to 400 ft below land surface. Relative-concentrations (sample concentrations divided by benchmark concentrations) were used for evaluating groundwater quality for those constituents that have Federal or California regulatory or non-regulatory benchmarks for drinking-water quality. A relative-concentration (RC) greater than 1.0 indicates a concentration above a benchmark. RCs for organic constituents (volatile organic compounds and pesticides) and special-interest constituents (perchlorate) were classified as "high" (RC is greater than 1.0), "moderate" (RC is less than or equal to 1.0 and greater than 0.1), or "low" (RC is less than or equal to 0.1). For inorganic constituents (major and minor ions, trace elements, nutrients, and radioactive constituents), the boundary between low and moderate RCs was set at 0.5. The assessments characterize untreated groundwater quality, not the quality of treated drinking water delivered to consumers by water purveyors; drinking-water benchmarks, and thus relative-concentrations, are used to provide context for the concentrations of constituents measured in groundwater. Aquifer-scale proportion was used in the status assessment as the primary metric for evaluating regional-scale groundwater quality. High aquifer-scale proportion is defined as the percentage of the area of the primary aquifer system with RCs greater than 1.0 for a particular constituent or class of constituents; moderate and low aquifer-scale proportions are defined as the percentages of the area of the primary aquifer system with moderate and low RCs, respectively. Percentages are based on an areal, rather than a volumetric basis. Two statistical approaches--grid-based, which used one value per grid cell, and spatially weighted, which used multiple values per grid cell--were used to calculate aquifer-scale proportions for individual constituents and classes of constituents. The spatially weighted estimates of high aquifer-scale proportions were within the 90% confidence intervals of the grid-based estimates for all constituents except iron. The status assessment showed that inorganic constituents had greater high and moderate aquifer-scale proportions in the Madera-Chowchilla study unit than did organic constituents. RCs for inorganic constituents with health-based benchmarks were high in 37% of the primary aquifer system, moderate in 30%, and low in 33%. The inorganic constituents contributing most to the high aquifer-scale proportion were arsenic (13%), uranium (17%), gross alpha particle activity (20%), nitrate (6.7%), and vanadium (3.3%). RCs for inorganic constituents with non-health-based benchmarks were high in 6.7% of the primary aquifer system, and the constituent contributing most to the high aquifer-scale proportion was total dissolved solids (TDS). RCs for organic constituents with health-based benchmarks were high in 10% of the primary aquifer system, moderate in 3.3%, and low in 40%; organic constituents were not detected in 47% of the primary aquifer system. The fumigant 1,2-dibromo-3-chloropropane (DBCP) was the only organic constituent detected at high RCs. Seven organic constituents were detected in 10% or more of the primary aquifer system: DBCP; the fumigant additive 1,2,3-trichloropropane; the herbicides simazine, atrazine, and diuron; the trihalomethane chloroform; and the solvent tetrachloroethene (PCE). RCs for the special-interest constituent perchlorate were moderate in 20% of the primary aquifer system. The second component of this study, the understanding assessment, identified the natural and human factors that may affect groundwater quality by evaluating statistical correlations between water-quality constituents and potential explanatory factors, such as land use, position relative to important geologic features, groundwater age, well depth, and geochemical conditions in the aquifer. Results of the statistical evaluations were used to explain the distribution of constituents in the study unit. Depth to the top of perforations in the well and groundwater age were the most important explanatory factors for many constituents. High and moderate RCs of nitrate, uranium, and TDS and the presence of herbicides, trihalomethanes, and solvents were all associated with depths to the top of perforations less than 235 ft and modern- and mixed-age groundwater. Positive correlations between uranium, bicarbonate, TDS, and the proportion of calcium and magnesium in the total cations suggest that downward movement of recharge from irrigation water contributed to the elevated concentrations of these constituents in the primary aquifer system. High and moderate RCs of arsenic were associated with depths to the top of perforations greater than 235 ft, mixed- and pre-modern-age groundwater, and location in sediments from the Chowchilla River alluvial fan, suggesting that increased residence time and appropriate aquifer materials were needed for arsenic to accumulate in the groundwater. High and moderate RCs of fumigants were associated with depths to the top of perforations of less than 235 ft and location south of the city of Madera; low RCs of fumigants were detected in wells dispersed across the study unit with a range of depths to top of perforations.