In most cases, the NPDES permitting program applies only to direct discharges to surface waters. Some cases in which discharges to ground water are directly hydrologically connected to a surface water have been incorporated into the NPDES program.

A wide variety of manmade conveyances are considered point sources, including pipes, ditches, channels, tunnels, certain kinds of ships, and offshore oil rigs.

NPDES permits cover industrial and municipal discharges, discharges from storm sewer systems in larger cities, storm water associated with numerous kinds of industrial activity, runoff from construction sites disturbing more than one acre, mining operations, and animal feedlots and aquaculture facilities above certain thresholds.

Special Exemptions

A number of types of discharges that meet the definition of a "point" source are not required to obtain an NPDES permit because of either statutory (congressional) or administrative (EPA) exemptions. These include the following:

• Some abandoned mines on nonfederal lands (state, local, private).
• Sewage (not other types of discharges) from ships covered by EPA's Vessel Sewage Discharge Program.
• Return flows from irrigated agriculture.
• Most drainage ditches associated with logging roads.
• Most smaller feedlots and aquaculture facilities.

Also, all so-called "indirect" dischargers are not required to obtain NPDES permits. The drawing explains the difference between "direct" and "indirect" discharges. An indirect discharger is one that sends its wastewater into a city sewer system, so it eventually goes to a sewage treatment plant (POTW). Though not regulated under NPDES, "indirect" discharges are covered by another CWA program, called pretreatment. "Indirect" dischargers send their wastewater into a city sewer system, which carries it to the municipal sewage treatment plant, through which it passes before entering a surface water.