All segments of San Francisco Bay were listed as impaired by certain polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) compounds in the 1998 and 2002 Clean Water Act Section 303(d) lists. The impetus for the listing was an interim advisory on the consumption of fish from the Bay issued by the California Office of Environmental Health Hazard Assessment. The advisory was issued after PCDD/F compounds and other pollutants (e.g., mercury and PCBs) were found in Bay fish tissue at levels thought to potentially pose a health risk to people consuming them. The Water Board opposed the 1998 listing of PCDD/Fs in the Bay but was overruled by the United States Environmental Protection Agency (USEPA).

Since FY 01-02, the Program has developed work plans and other work products to characterize PCDD/F compounds and to provide relevant information regarding their relation to storm water runoff. To coordinate and plan activities related to PCDD/F compounds and other pollutants of concern, the Program continues to work with other Bay area dischargers and Water Board staff through BASMAA, the Clean Estuary Partnership and the Regional Monitoring Program. Work plans and other work products developed to address the control of dioxin compounds include: