The site is located in the Upper San Pedro River Basin, bounded by several mountain ranges including the Whetstone Mountains to the west, the Dragoon Mountains to the east, the Huachuca Mountains to the southwest and the Mule mountains to the southeast.

The San Pedro River drains approximately 2,500 square miles, of which 700 are in Mexico. The river flows northward from Mexico and joins the Gila River near Winkelman, Arizona. The river is perennial where it intersects the water table, supporting a rich riparian ecosystem. 



At the site, there’s a shallow aquifer and a deep regional aquifer with wells exhibiting artesian conditions. Some wells in the St. David area actually flow at the surface. In addition, there is a small perched zone on ANPI's property that resulted from wastewater discharges to unlined washes and ponds. Until recently, the perched zone drained into the shallow aquifer and was a source of nitrate and perchlorate contamination in the shallow aquifer in the southern area of the site. However, this perched zone is now nearly dry and no longer discharges to the shallow aquifer.



In the southern area of the site, the shallow aquifer is further divided into the Molinas Creek Sub-Aquifer and the alluvial aquifer associated with the San Pedro River. Nitrate and perchlorate groundwater contamination only occurs in the Molinas Creek Sub-Aquifer and the perched zone. Perchlorate has never been detected in the shallow alluvial aquifer associated with the San Pedro River or in the river itself. The groundwater flow direction in the shallow aquifer is generally northward (sub-parallel to the river). However, the Molinas Creek Sub-Aquifer appears to have almost no flow due to its apparent hydraulic isolation from the rest of the shallow aquifer.