Water quality standards in the southern portion of San Francisco Bay were being exceeded in spite of the point source controls in place at water treatment facilities. A watershed-wide assessment addressed both point and non-point pollutant sources, such as urban runoff, upstream inputs, air deposition, and sediment resuspension. The Copper and Nickel TMDL Work Group, comprised of stakeholders from wastewater and stormwater dischargers, environmental groups, industry, regulatory agencies, and other involved citizens, was formed to provide guidance for the development of the TMDLs for copper and nickel in the South Bay. The key finding of the assessment was that impairment to beneficial uses of the South Bay due to ambient copper and nickel concentrations was unlikely. Largely as a result of this work, the San Francisco Bay Regional Water Quality Control Board approved a Basin Plan Amendment in 2002 that includes higher site-specific objectives in the Lower South San Francisco Bay.