The Madera-Chowchilla study unit is about 860 square miles and consists of the Madera and Chowchilla groundwater subbasins of the San Joaquin Valley Basin (California Department of Water Resources, 2003; Shelton and others, 2009). The study unit has hot, dry summers and cool, moist winters. Average annual rainfall ranges from 11 to 15 inches, most of which occurs between November and February. The main surface-water features in the study unit are the San Joaquin, Fresno, and Chowchilla Rivers, and the Madera and Chowchilla canals. Land use in the study unit is about 69 percent (%) agricultural, 28% natural (mainly grasslands), and 3% urban. The primary crops are orchards and vineyards. The largest urban area is the city of Madera.

The primary aquifer system is defined as those parts of the aquifer corresponding to the perforated intervals of wells listed in the California Department of Public Health (CDPH) database. In the Madera-Chowchilla study unit, these wells typically are drilled to depths between 200 and 800 feet, consist of a solid casing from land surface to a depth of about 140 to 400 feet, and are perforated below the solid casing. Water quality in the primary aquifer system may differ from that in the shallower and deeper parts of the aquifer system.

The primary aquifer system in the study unit consists of Quaternary-age alluvial-fan and fluvial deposits that were formed by the rivers draining the Sierra Nevada. Sediments consist of gravels, sands, silts, and clays and generally are coarser closest to the Sierra Nevada and become finer towards the center of the basin. The structure and composition of the deposits in the Madera-Chowchilla study unit are different from those in other parts of the eastern San Joaquin Valley because the Fresno and Chowchilla Rivers primarily drain the Sierra Nevada foothills, whereas the larger rivers drain higher elevations with greater sediment supply. These differences in the sources of sediments are important because they may affect the groundwater chemistry and the physical structure of the sedimentary deposits. Some of the clay layers are lacustrine deposits, the most extensive of which, the Corcoran Clay, underlies the western part of the study unit and divides the primary aquifer system into an unconfined to semi-confined upper system and a largely confined lower system.

Regional lateral flow of groundwater is southwest towards the valley trough. Irrigation return flows are the major source of groundwater recharge, and groundwater pumping is the major source of discharge. Groundwater on a lateral flow path may be repeatedly extracted by pumping wells and reapplied at the surface multiple times before reaching the valley trough, resulting in a substantial component of downward vertical flow (Burow and others, 2004; Phillips and others, 2007; Faunt, 2009). This flow pattern enhances movement of water from shallow depths to the primary aquifer system.