Individual NJPDES permits are issued to facilities that cannot eliminate exposure of pollutants to stormwater. These facilities have to develop and implement Stormwater Pollution Prevention Plans to minimize or eliminate contact between pollutants and stormwater. Other permit conditions may require monitoring stormwater discharges for pollutants, and in some cases, effluent limitations may be imposed.

For discharges of sanitary wastewater over 2,000 GPD from various disposal methods, such as septic systems lagoons, spray irrigation, or overland flow, a sanitary wastewater permit provides the necessary management practices and monitoring requirements to ensure conformance with the NJDPES regulations and the Ground Water Quality Standards.

Discharges of industrial wastewater, such as cooling water, process wastewater, and boiler blowdown require a permit for the particular disposal method employed by the facility (lagoon, spray irrigation, overland flow, etc.) to ensure conformance with the NJPDES regulations and the Ground Water Quality Standards through management practices and monitoring.

Systems classified as underground injection system dispose of wastewater directly into the subsurface. These subsurface disposal systems include disposal beds or trenches, dry wells and seepage pits and can receive sanitary or industrial wastewater. UIC discharges are regulated via permits to protect underground sources of drinking water and ensure compliance with state performance standards as well as the Ground Water Quality Standards.

The injection of potable water for future recovery into aquifers requires a permit to ensure compliance with management practices of the injection process and with the ground water quality standards.