Many types of industry use water in their manufacturing processes, which then results in large discharges of wastewater. This effluent can be a potential source of pollution affecting groundwater. For this reason, industrial sites that discharge wastewater either directly to the aquifer or to the nearby land surface are required to apply to ADEQ for an Aquifer Protection Permit (APP).

If the discharge is to a surface water body, an AZPDES permit is also required. An industrial facility (non-construction) may also be regulated by the AZPDES stormwater program. In this program, a Multi-Sector General Permit is required of certain industrial facilities to discharge stormwater from a site.