The goal of this study is to determine the impact of various operating factors on membrane fouling in activated sludge membrane bioreactor (MBR) process, typically used for water reclamation. In this process, ultrafiltration (UF) and microfiltration (MF) hollow fiber membranes, submerged in the bioreactor, provided a solid—liquid separation by replacing gravity settling. Activated sludge from a food wastewater treatment plant was inoculated to purify synthetic wastewater consisting of glucose and (NH4)2SO4 as a source of carbon and nitrogen, respectively. The results clearly showed that membrane fouling, defined as permeate flux decline due to accumulation of substances within membrane pores and/or onto membrane surface, was greatly influenced by membrane type and module configuration. It was also found that the rate and extent of permeate flux decline increased with increasing suction pressure (or initial operating flux) and with decreasing air-scouring rate. The mixed liquor suspended solids (MLSS) concentrations, however, exhibited very little influence on permeate flux for the range of 3600–8400 mg/L. Another important finding of this investigation was that non-continuous membrane operation significantly improved membrane productivity. This observation can be explained by the enhanced back transport of foulants under pressure relaxation. During non-suction periods, the foulants not irreversibly attached to the membrane surface, diffused away from the membrane surface because of concentration gradient. Furthermore, the effectiveness of air scouring was greatly enhanced in the absence of transmembrane suction pressure, resulting in higher removal of foulants accumulated on the membrane surface. The use of intermittent suction operation may not be economically feasible at large-scale, but it may offer an effective fouling control means for small-scale MBR processes treating wastewaters with high fouling potential.