Membrane bioreactors (MBRs) have been used increasingly for municipal wastewater treatment. The current wastewater treatment plants are designed to treat three times the average flow in dry weather (DWF) which covers the expected range of incoming flow rates. If throughput in MBRs can be changed readily by changing the energy input into the system, a smaller plant can be designed. Under varying throughput operation, a high aeration rate is required to generate a high crossflow velocity to minimize fouling. At low flow rates, a low aeration rate is used to minimize energy consumption. The aim of this work is to explore the feasibility of designing smaller membrane plants by varying the throughput. This requires the control of membrane fouling, so that chemical cleaning is not compromised. Fouling is controlled by limiting the membrane flux and also by flushing the surface of the membranes with large air bubbles. Variations of the permeate flux and the aeration rate were varied in this study and their effect on controlling fouling noted. Intermittent permeation while retaining aeration was found to be an effective technique for long-term sustainability of high fluxes.