Wastewater flows from the east side of the City are transported to the Southeast Wastewater Treatment Plant (SEP), which is located on Phelps Street between Jerrold and Evans Avenues. During dry weather, wastewater flows consist mainly of municipal and industrial sanitary sewage and wastewater, which is all treated to a secondary level at the SEP. The treated wastewater is then discharged to the Bay through the deep water outfall at Pier 80, immediately to the north of the Islais Creek Channel.

During wet weather, the combined sewerage system collects large volumes of stormwater runoff in addition to municipal and industrial wastewater, and is conveyed to treatment facilities before eventual discharge to the Bay. Depending on the amount of rainfall, wet weather flows are treated to varying levels before discharge to the Bay. Up to 150 mgd of wet weather flows receive secondary treatment at the SEP. The Plant can also treat up to an additional 100 mgd to a primary treatment standard plus disinfection. Treated wet weather discharges from SEP occur through the Pier 80 outfall directly to the Bay or through the Quint Street outfall to Islais Creek Channel. Only wastewater treated to a secondary level is discharged at the Quint Street outfall.

Up to an additional 100 mgd of wet weather flows receive primary treatment plus disinfection at the North Point Wet Weather Facility, located on the north side of the City at 111 Bay Street, which operates only during wet weather. Treated effluent from this facility is discharged through four deep water outfalls, approximately 800 feet from the Bay shore and 18 feet below mean lower low water level. Two of the deep water outfalls terminate at the end of Pier 33 and two terminate at the end of Pier 35 on the northeastern Bay shore.