In 1972, the Clean Water Act established environmental programs that included the National Pollutant Discharge Elimination System (NPDES) program. The Clean Water Act gives EPA the authority to set limits on a water quality basis and to require an NPDES permit prior to the discharge of pollutants. Stormwater discharge permits provide a mechanism for monitoring the discharge of pollutants to 'waters of the U.S.' and for establishing appropriate controls. EPA can delegate permit programs to state governments. In Nebraska, NDEQ is the agency that implements this program and issues NPDES permits.
The NPDES stormwater permit program was issued in two phases. Lincoln and Omaha were both issued permits under Phase I of the program. Lincoln's permit was issued effective September 2002. Phase II of the program required permits for smaller urban areas and added additional requirements for all affected communities. In Nebraska, a total of 20 cities and four counties currently must have NPDES stormwater permits.