Groundwater quality in the approximately 3,900-square-mile (mi2) San Diego Drainages Hydrogeologic Province (hereinafter San Diego) study unit was investigated from May through July 2004 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The study unit is located in southwestern California in the counties of San Diego, Riverside, and Orange. 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 GAMA San Diego study was designed to provide a statistically robust assessment of untreated-groundwater quality within the primary aquifer systems. The assessment is based on water-quality and ancillary data collected by the USGS from 58 wells in 2004 and water-quality data from the California Department of Public Health (CDPH) database. The primary aquifer systems (hereinafter referred to as the primary aquifers) were defined by the depth interval of the wells listed in the California Department of Public Health (CDPH) database for the San Diego study unit. The San Diego study unit consisted of four study areas: Temecula Valley (140 mi2), Warner Valley (34 mi2), Alluvial Basins (166 mi2), and Hard Rock (850 mi2). The quality of groundwater in shallow or deep water-bearing zones may differ from that in the primary aquifers. For example, shallow groundwater may be more vulnerable to surficial contamination than groundwater in deep water-bearing zones. This study had two components: the status assessment and the understanding assessment. The first component of this study-the status assessment of the current quality of the groundwater resource-was assessed by using data from samples analyzed for volatile organic compounds (VOC), pesticides, and naturally occurring inorganic constituents, such as major ions and trace elements. The status assessment is intended to characterize the quality of groundwater resources within the primary aquifers of the San Diego study unit, not the treated drinking water delivered to consumers by water purveyors. The second component of this study-the understanding assessment-identified the natural and human factors that affect groundwater quality by evaluating land use, well construction, and geochemical conditions of the aquifer. Results from these evaluations were used to help explain the occurrence and distribution of selected constituents in the study unit. Relative-concentrations (sample concentration divided by benchmark concentration) were used as the primary metric for relating concentrations of constituents in groundwater samples to water-quality benchmarks for those constituents that have Federal and (or) California benchmarks. For organic and special-interest constituents, relative-concentrations were classified as high (> 1.0), moderate (> 0.1 and ≤1.0), and low (≤0.1). For inorganic constituents, relative concentrations were classified as high (> 1.0), moderate (> 0.5 and ≤1.0), and low (≤0.5). Grid-based and spatially weighted approaches were then used to evaluate the proportion of the primary aquifers (aquifer-scale proportions) with high, moderate, and low relative-concentrations for individual compounds and classes of constituents. One or more of the inorganic constituents with health-based benchmarks were high (relative to those benchmarks) in 17.6 percent of the primary aquifers in the Temecula Valley, Warner Valley, and Alluvial Basins study areas (hereinafter also collectively referred to as the Alluvial Fill study areas because they are composed of alluvial fill aquifers), and in 25.0 percent of the Hard Rock study area. Inorganic constituents with health-based benchmarks that were frequently detected at high relative-concentrations included vanadium (V), arsenic (As), and boron (B). Vanadium and As concentrations were not significantly correlated to either urban or agricultural land use indicating natural sources as the primary contributors of these constituents to groundwater. The positive correlation of B concentration to urban land-use was significant which indicates that anthropogenic activities are a contributing source of B to groundwater. The correlation of V, As and B concentrations to pH was positive, indicating that in alkaline groundwater these constituents are being desorbed from, or being inhibited from adsorbing to, particle surfaces. Inorganic constituents with aesthetic benchmarks that were detected at high relative-concentrations include manganese (Mn), iron (Fe), and total dissolved solids (TDS). In the Alluvial Fill study areas, Mn and TDS were detected at high relative-concentrations in 13.7 percent of the primary aquifers, and Fe in 6.9 percent. In the Hard Rock study area, Mn was detected at high relative-concentrations in 33.3 percent of the primary aquifers, and TDS in 16.7 percent; Fe was not detected at high relative-concentrations. Total dissolved solids concentrations were significantly correlated to agricultural land use suggesting that agricultural practices are a contributing source of TDS to groundwater. Manganese and Fe concentrations were highest in groundwater with low dissolved oxygen and pH indicating that the reductive dissolution of oxyhydroxides may be an important mechanism for the mobilization of Mn and Fe in groundwater. TDS concentrations were highest in shallow wells and in modern (< 50 yrs) groundwater which indicates anthropogenic activities as a source of TDS concentrations in groundwater. The relative-concentrations of organic constituents with health-based benchmarks were high in 3.0 percent of the primary aquifers in the Alluvial Fill study areas. A single detection in the Alluvial Basins study area of the discontinued gasoline oxygenate methyl tert-butyl ether (MTBE) was the only organic constituent detected at a high relative-concentration; high relative-concentrations of these constituents were not detected in the Hard Rock study area. Twelve of 88 VOCs and 14 of 123 pesticides and pesticide degradates analyzed in grid wells were detected. Chloroform was the only VOC detected in more than 10 percent of the grid wells. The herbicides simazine, atrazine, and prometon were each detected in greater than 10 percent of the grid wells. Perchlorate was detected in 22 percent of the grid wells sampled. The understanding assessment showed a significant correlation of trihalomethanes (THMs) and solvents to urban land-use, indicating that detections of these constituents are more likely to occur in groundwater underlying urbanized areas of the study unit. MTBE concentrations were negatively correlated to the distance from the nearest leaking underground fuel tank, indicating that point sources are the most significant contributing factor for MTBE concentrations to groundwater in the study unit. The positive correlation of THM and herbicide concentrations to modern groundwater was significant, as was the negative correlation of herbicide concentrations to pH and anoxic groundwater. The negative correlation of herbicides to pH and anoxic groundwater was likely due to the fact that these constituents were detected more frequently in shallow wells where groundwater conditions tend to be oxic with relatively low pH.