Factors affecting filtration performance were investigated in a sequencing batch reactor (SBR) coupled with a submerged microfiltration module. Special bioreactors for aerobic and anoxic phases were specifically designed in order to differentiate the effect of dissolved oxygen (DO) from that of mixing intensity, on membrane filterability. When the filterability of a submerged microfilter was examined at each SBR phase, DO concentration, as well as mixing intensity proved to have a major influence on the membrane performance regardless of the SBR phase. A higher DO concentration resulted in a slower rise in TMP, corresponding to less membrane fouling, which was investigated in depth through a series of analyses including resistance measurements and compressibility of the cake layer as well as particle sizes as a functions of DO for both aerobic and anoxic phases in SBR.