The Yakima River basin aquifer system underlies about 6,200 square miles in south-central Washington. The aquifer system consists of basin-fill deposits occurring in six structural-sedimentary basins, the Columbia River Basalt Group (CRBG), and generally older bedrock. The basin-fill deposits were divided into 19 hydrogeologic units, the CRBG was divided into three units separated by two interbed units, and the bedrock was divided into four units (the Paleozoic, the Mesozoic, the Tertiary, and the Quaternary bedrock units). The thickness of the basin-fill units and the depth to the top of each unit and interbed of the CRBG were mapped. Only the surficial extent of the bedrock units was mapped due to insufficient data. Average mapped thickness of the different units ranged from 10 to 600 feet. Lateral hydraulic conductivity (Kh) of the units varies widely indicating the heterogeneity of the aquifer system. Average or effective Kh values of the water-producing zones of the basin-fill units are on the order of 1 to 800 ft/d and are about 1 to 10 ft/d for the CRBG units as a whole. Effective or average Kh values for the different rock types of the Paleozoic, Mesozoic, and Tertiary units appear to be about 0.0001 to 3 ft/d. The more permeable Quaternary bedrock unit may have Kh values that range from 1 to 7,000 ft/d. Vertical hydraulic conductivity (Kv) of the units is largely unknown. Kv values have been estimated to range from about 0.009 to 2 ft/d for the basin-fill units and Kv values for the clay-to-shale parts of the units may be as small as 10-10 to 10-7 ft/d. Reported Kv values for the CRBG units ranged from 4x10-7 to 4 ft/d. Variations in the concentrations of geochemical solutes and the concentrations and ratios of the isotopes of hydrogen, oxygen, and carbon in groundwater provided information on the hydrogeologic framework and groundwater movement. Stable isotope ratios of water (deuterium and oxygen-18) indicated dispersed sources of groundwater recharge to the CRBG and basin-fill units and that the source of surface and groundwater is derived from atmospheric precipitation. The concentrations of dissolved methane were larger than could be attributable to atmospheric sources in more than 80 percent of wells with measured methane concentrations. The concentrations of the stable isotope of carbon-13 of methane were indicative of a thermogenic source of methane. Most of the occurrences of methane were at locations several miles distant from mapped structural fault features, suggesting the upward vertical movement of thermogenic methane from the underlying bedrock may be more widespread than previously assumed or there may be a more general occurrence of unmapped (buried) fault structures. Carbon and tritium isotope data and the concentrations of dissolved constituents indicate a complex groundwater flow system with multiple contributing zones to groundwater wells and relative groundwater residence time on the order of a few tens to many thousands of years. Potential mean annual recharge for water years 1950-2003 was estimated to be about 15.6 in. or 7,149 ft3/s (5.2 million acre-ft) and includes affects of human activities such as irrigation of croplands. If there had been no human activities (predevelopment conditions) during that time period, estimated recharge would have been about 11.9 in. or 5,450 ft3/s (3.9 million acre-ft). Estimated mean annual recharge ranges from virtually zero in the dry parts of the lower basin to more than 100 in. in the humid uplands, where annual precipitation is more than 120 in. Groundwater in the different hydrogeologic units occurs under perched, unconfined, semiconfined, and confined conditions. Groundwater moves from topographic highs in the uplands to topographic low areas along the streams. The flow system in the basin-fill units is compartmentalized due to topography and geologic structure. The flow system also is compartmentalized for the CRBG units but not to as large