In 1972 Congress adopted the federal Clean Water Act which requires pollutant discharges to navigable waters to be authorized by a National Pollutant Discharge Elimination System (NPDES) permit. Amendments to the act in 1987 include a section which required regulation of municipal and industrial storm water dischargers. It also required that individual control strategies (ICS) be developed by the storm water dischargers, to impose controls on nonpoint sources of pollution. This was in order to achieve compliance with water quality standards for "impaired" bodies of water. In 1989 the State Water Resources Control Board listed the south San Francisco Bay as impaired because water quality standards for heavy metals were frequently exceeded.
The Basin Plan issued by the Regional Water Quality Control Board (Regional Board) in 1986 and its subsequent amendments, would later require the Program to submit proposals for determining pollutant loading, sources and control measures for nonpoint source pollution to the south San Francisco Bay.
Recognizing that the proposed federal and state regulations would affect them all, north Santa Clara Valley's 13 cities, Santa Clara County and the Santa Clara Valley Water District - all jurisdictions which contribute runoff to the South Bay - joined forces to apply for a joint NPDES municipal storm water permit, rather than 15 separate ones.
In June of 1990 the Environmental Protection Agency (EPA) conditionally ruled that the NPDES permit satisfied the Clean Water Act's requirement for an ICS. The NPDES Permit was reissued in 1996 by the State Water Resources Control Board, on behalf of the US/EPA. The 2000 re-issuance of the NPDES Permit occurred in 2001 by the RWQCB.