The Clean Water Act prohibits anybody from discharging "pollutants" through a "point source" into a "water of the United States" unless they have an NPDES permit. The permit will contain limits on what you can discharge, monitoring and reporting requirements, and other provisions to ensure that the discharge does not hurt water quality or people's health. In essence, the permit translates general requirements of the Clean Water Act into specific provisions tailored to the operations of each person discharging pollutants.

The term "pollutant" is defined very broadly in the Clean Water Act . It includes any type of industrial, municipal, and agricultural waste discharged into water. Some examples are dredged soil, solid waste, incinerator residue, sewage, garbage, sewage sludge, munitions, chemical wastes, biological materials, radioactive materials, heat, wrecked or discarded equipment, rock, sand, cellar dirt and industrial, municipal, and agricultural waste. By law, a pollutant is not sewage from vessels or discharges incidental to the normal operation of an Armed Forces vessel, or certain materials injected into an oil and gas production well.

The term "point source" is also defined very broadly in the Clean Water Act because it has been through 25 years of litigation. It means any discernible, confined and discrete conveyance, such as a pipe, ditch, channel, tunnel, conduit, discrete fissure, or container. It also includes vessels or other floating craft from which pollutants are or may be discharged. By law, the term "point source" also includes concentrated animal feeding operations, which are places where animals are confined and fed. By law, agricultural stormwater discharges and return flows from irrigated agriculture are not "point sources".

The term "water of the United States" is also defined very broadly in the Clean Water Act and after 25 years of litigation. It means navigable waters, tributaries to navigable waters, interstate waters, the oceans out to 200 miles, and intrastate waters which are used: by interstate travelers for recreation or other purposes, as a source of fish or shellfish sold in interstate commerce, or for industrial purposes by industries engaged in interstate commerce.