A wastewater treatment system is provided that includes first and second reactors, each operative to nitrify or denitrify wastewater contained therein. Downstream from the first and second reactors is a membrane reactor that operates under aerobic conditions and includes one or more submersed membranes for separating solids. Extending between the membrane reactor and each of the first and second reactors is a return activated sludge line with appropriate controls for permitting return activated sludge to be directed to one of the reactors at a time. To nitrify and denitrify wastewater, a wastewater influent stream is alternatively directed to the anoxic reactors which are alternatively operated under aerobic and anoxic conditions so as to nitrify or denitrify the wastewater contained therein. To reduce or minimize the dissolved oxygen return from the membrane reactor to the first and second reactors, the flow of return activated sludge is controlled such that generally return activated sludge is returned to the reactor operating under aerobic conditions.