The behavior of a University of Cape Town (UCT) membrane bioreactor (MBR) system was investigated for use in biological nutrient removal from real wastewater. The pilot plant was in operation for a period of 165 days, during which an extensive data gathering campaign was conducted. The pilot plant was started up by inoculating it with activated sludge from a nearby wastewater treatment plant, and it was fed by real municipal wastewater characterized by high organic nitrogen concentrations attributable to discharges from industrial wastewater and sporadic landfill leachate. Carbon and biological nutrient removal processes, a sludge production process, and a membrane fouling mechanism were analyzed and discussed. The organic nitrogen levels, which were higher than typical values for municipal wastewater, caused ammonification phenomena. This led to intense nitrification and denitrification activities. The pilot plant showed satisfactory efficiency in terms of average removal efficiencies for both carbon and nitrogen. However, lower efficiencies were recorded for phosphorus removal as an indirect effect of the intense denitrifying activity of the phosphorus-accumulating organisms in the anoxic tank. Membrane fouling was mainly of reversible nature, and low values of soluble microbial product were measured.