The City and County of San Francisco discharges an average of 18 MGD (dry weather flow) of treated municipal wastewater into the Pacific Ocean approximately 6 km offshore. Receiving water environmental monitoring data have been collected from 1982 to present, spanning periods of pre-discharge, discharge of primary treated effluent, and discharge of secondary treated effluent. Using ordination and BACI (before-after-control-impact) analysis techniques, we examine shifts in the benthic infauna community to determine if the discharge is having an impact on the receiving water environment. The primary community gradients showed shifts likely due to large scale oceanographic conditions, including several Fl Ni (n) over tilde o (ENSO) events. The BACI analyses revealed that one of the gradients also captures a shift in biota at the impact stations, but not at the reference station, during the period of primary effluent discharge. After the commencement of secondary effluent discharge, the community structure shifted back to resemble the reference station again. Multiple regression analysis showed that this biological shift corresponds to temporal changes in effluent mass loading of solids. Although this study showed some evidence of an outfall effect, the sampling design is inadequate to answer a number of management questions relative to effluent discharge, and it cannot address confounding factors, including impact of outflow from San Francisco Bay. A new sampling design that addresses these problems is discussed.