The Pinal Creek Basin is bounded by the Pinal Mountains to the south and by the Apache Peaks and Globe Hills to the east. The setting is a typical basin and range structure that has northwest-trending ranges of igneous and metamorphic rocks separated by a valley that is filled with alluvial deposits. Consolidated and semi-consolidated basin-fill deposits (known as the Gila Conglomerate) that occur in Pinal Creek were created by late Cenozoic block faulting. Unconsolidated alluvium overlies the Gila Conglomerate and ranges from 300 to 800 meters wide and may be as thick as 50 meters. Major surface water bodies in the basin include Bloody Tanks Wash and Russell Gulch, which join to form Miami Wash, which flows northward into Pinal Creek.

There are two principal aquifers in the basin: the regional Gila Conglomerate aquifer and the shallow alluvial aquifer. The Gila Conglomerate aquifer is the main source of water for domestic and industrial use. The Gila Conglomerate contains significant quantities of calcium carbonate which can neutralize acidic water, and is much less permeable than the alluvial aquifer, both of which have helped to protect it from extensive contamination. Contamination by acid-metal bearing water is largely localized within the alluvial aquifer.

Surface water in the basin is mostly ephemeral occurring only in response to precipitation events. Perennial flow in Pinal Creek begins at the north end of the channel where the groundwater table intersects the surface due to a truncation of the alluvial and Gila Conglomerate aquifers by bedrock.