The U.S. Geological Survey and Sonoma County Water Agency (SCWA) are engaged in a cooperative project to characterize the hydrogeology of southern Sonoma Valley, a groundwater basin in the northern California Coast Ranges where groundwater represents about 60% of the valley’s water supply. The basin lies near the Sonoma volcanic field and major transverse faults of the San Francisco Bay region, resulting in a complex aquifer system comprising volcanic and sedimentary rocks and unconsolidated sediments that are cut by faults and overlain to the south by recent Bay Muds of San Francisco Bay. Geologic sections were constructed using geologic maps and lithologic data from over 1,500 water wells compiled by SCWA to describe the subsurface geologic configuration relative to groundwater pumping wells. This work suggests an aquifer system extending to about 900 feet below land surface (ft bls), consisting of upper and lower aquifer units separated by an intermediate unit with lower hydraulic conductivity, overlying and partly interfingering with a complex suite of volcanic rocks. SCWA constructed a four-layer hydrostratigraphic model of the basin using spatial trends in the lithologic data. The hydrostratigraphic layers defined by SCWA include multiple mapped geologic formations because of heterogeneity and complex interfingering between stratigraphic units. Water from selected wells was analyzed for specific conductance, major and minor ions, nutrients, stable isotopes, carbon isotopes, and tritium. Well data were categorized by completed perforation interval into shallow wells (< 200 ft bls), mid-depth wells (200–500 ft bls), and deep wells (> 500 ft bls). Shallow wells typically have water types related to recent mountain-front recharge, and, near the tidal marshlands north of San Pablo Bay, have high chloride and total dissolved solid concentrations associated with modern saline-water intrusion. Mid-depth and deep wells have water with poor water-quality, likely influenced by connate water from consolidated marine sediments, or a mixture of water from consolidated sediments and thermal water. This cooperative basin characterization of subsurface geology, hydrostratigraphy, and water chemistry will enable SCWA to make strategic water management decisions in Sonoma Valley.