Water levels in wells in some areas of Doña Ana County are decreasing, an indication that water is being pumped out faster than it is being replenished. Declining water levels are found mostly where water is being pumped from the Santa Fe Group basin deposits, such as in the region of Butterfield Park, east of Las Cruces and in the Jornada del Muerto Basin. Water level declines centered in the El Paso/Ciudad Juarez region, in the Hueco Basin, have also started to affect water levels in the southeast corner of Doña Ana County.

Despite the seemingly constant source of water from the Rio Grande, and the theoretically large reservoirs of water in the Santa Fe Group deposits, water resources in Doña Ana County are definitely not limitless. It appears that recharge to the Santa Fe Group aquifers occurs quite slowly, slower than the rate at which water is being pumped out. Also, the water in the Rio Grande floodplain aquifer is directly connected with the Rio Grande itself, pumping water from the ground affects the amount of flow in the river.

The quality of water in Doña Ana County is highly variable. The water in the aquifers ranges from fresh to slightly saline, depending on the characteristics of the rocks the water has flowed through. In general, ground water found near recharge zones and in the river tends to be fresh, and some shallow water in the floodplain deposits can be quite saline because of irrigation practices.

There are also several sources for ground-water pollution in Doña Ana County. Leaking underground petroleum storage tanks, septic tanks and cesspools, closed and active landfills, dairies and other agricultural industries, and agricultural pesticide and herbicide runoff, all of which are found in Doña Ana County, can have negative effects on ground-water quality. For the most part, however, the public water supply systems in Doña Ana County provide water of adequate quality.