A method and system is provided for treating wastewater. In one process, wastewater is directed into a treatment tank and biologically treated. The biologically treated wastewater is directed as mixed liquor from the treatment tank to a bottom portion of a downstream filtration tank having at least one submerged membrane module that extends across substantially the entire cross sectional area of the filtration tank mixed liquor is directed from the bottom of the filtration tank upwardly into the membrane module such that substantially all of the mixed liquor received in the bottom of the filtration tank flows through the membrane module. As the mixed liquor flows vertically through the membrane module, the method includes inducing at least some of the mixed liquor through walls of one or more membrane filters that form a part of the membrane module, producing a permeate stream. The remaining mixed liquor passing through and from the membrane module is referred to as a non-permeate stream and the non-permeate stream, or at least a substantial portion thereof, is recirculated to the treatment tank. The filtration tank is sized relative to the membrane module and the process is carried out such that there is no substantial recycle of mixed liquor in the filtration tank itself. Although mixed liquor may be recirculated from the filtration tank back to the treatment tank and then back to the filtration tank and so forth and so on, once the mixed liquor in the filtration tank makes one pass through the membrane module the mixed liquor is recycled back to the treatment tank and generally not permitted to be recycled back through the membrane module without first returning to the treatment tank.