The CWA, as it applies to mining, made it unlawful to discharge any pollutant from a point source into navigable waters, unless a permit was obtained. EPA's National Pollutant Discharge Elimination System (NPDES) permit program controls discharges (Section 402 of the CWA). Point sources are discrete conveyances such as pipes or man-made ditches.

The Army Corps of Engineers (Corps) is responsible for authorizing the placement of material from mining operations into streams and wetlands. Under section 404 of the Clean Water Act (CWA), the Corps may only grant permits authorizing surface mining when no more than minimal adverse environmental effects result from the activity.  The CWA and all subsequent permitting is ultimately regulated by the federal Office of Surface Mining (OSM).  Individual states enforce and are allowed to add to these regulations with permission of the federal government.  States with primacy directly enforce the CWA and its subsequent permits.