Methods and apparatus for treating wastewater are described, one method embodiment including the steps of flowing a mixed liquor suspended solids to a high rate clarification stage, forming a clarifier effluent, a first waste activated sludge stream, and a return waste activated sludge stream. The high rate clarifier effluent stream then flows to a membrane stage that includes a membrane media, producing a membrane reject (retentate) stream and a treated effluent (permeate) stream. Optionally, the methods include routing a screened raw wastewater to an anaerobic and/or aerated anoxic stage and introducing a gas comprising oxygen to the wastewater during the aerated anoxic stage, and optionally allowing the product of this stage to flow to an aeration stage prior to the high rate clarification stage.