The North San Francisco Bay study unit is approximately 1,000 square miles and consists of the Wilson Grove Formation Highlands, Alexander Valley, Santa Rosa Valley, Petaluma Valley, Lower Russian River Valley, Kenwood Valley, Volcanic Highlands, and Napa-Sonoma Valley groundwater basins (California Department of Water Resources, 2003). These basins were grouped into three study areas primarily on the basis of geology. The alluvium-filled valleys were combined to form the Valleys and Plains study area; the Wilson Grove Formation Highlands and the Volcanic Highlands were designated as the other two study areas (Kulongoski and others, 2006).

The study unit has warm, dry summers and cool, moist winters. Average annual rainfall is 30 inches. The study areas are drained by several rivers and their principal tributaries. The primary aquifers consist of alluvial sediments (mixtures of sand, silt, clay, cobbles, and boulders), marine deposits (fossiliferous sandstones containing lenses of conglomerate and sandy shale), and volcanic deposits (pumice tuff, tuff breccias). The primary aquifers are defined as those parts of the aquifers corresponding to the perforated intervals of wells listed in the California Department of Public Health database. Public-supply wells are typically drilled to depths between 200 and 500 feet, consist of solid casing from the land surface to a depth of about 60 to 200 feet, and are perforated below the solid casing. Water quality in the shallower and deeper parts of the aquifer system may differ from that in the primary aquifers.

Land use in the study unit is approximately 55 percent (%) natural (mostly grasslands and forests), 31% agricultural, and 14% urban. The primary agricultural uses are for pasture, hay, vineyards, flowers, nurseries, and orchards. The largest urban areas are the cities of Santa Rosa, Petaluma, Rohnert Park, Windsor, and Napa.

Municipal water use accounts for nearly half of the total water use in the study unit; the remainder is used for irrigated agriculture. Groundwater accounts for about a quarter of the municipal supply, depending on the area, and surface water accounts for the remainder. Recharge to groundwater is primarily stream-channel infiltration from the major rivers and their tributaries, and infiltration of water from precipitation and irrigation. The primary sources of discharge are water pumped for irrigation and municipal supply, evaporation, and discharge to streams.