Initial efforts to improve water quality under the NPDES program primarily focused on reducing pollutants in industrial process wastewater and discharges from municipal sewage treatment plants. However, as pollution control measures for these sources were implemented and refined, studies indicated that more diffuse sources of water pollution were also significant causes of water quality impairment; specifically, storm water runoff draining large surface areas from agricultural and urban land.

The Federal Water Quality Act of 1987 recognized that runoff from these urban areas and industrial sites contributed to the pollution of surface waters. It required the U.S. Environmental Protection Agency (EPA) to address storm water discharges using a two-phased approach. The Phase I final regulations were published in November of 1990. The Phase II final regulations were published in December of 1999.

• In Phase I, the EPA required medium to large municipal separate storm sewer systems (MS4) operators to obtain permit coverage. These MS4s generally served areas with populations of 100,000 or more. Dischargers of "storm water discharges associated with industrial activity" were also required to apply for permits.
• Phase II regulates small municipal separate storm sewer system (Small MS4) discharges in Urban Areas (UA), storm water discharge associated with small construction activity, and municipally owned industrial activities. A "small" MS4 is any MS4 not already covered by Phase I of the NPDES Storm Water program. Numerous communities in New England have been designated as falling within EPA's urban area definition.