This section is responsible for implementing the National Pollutant Discharge Elimination System. This takes the form of issuing discharge permits for industries and municipalities that discharge or dispose of treated wastewater.

For industrial facilities, permits are available for discharges, surface impoundment disposal, and land application. Several general permits are now available for specific types of industries.

For municipal facilities, permits are available for discharges. A general permit is now available for those municipalities that discharge from a lagoon system.

Application forms for municipal and industrial facilities are available.