A membrane filtration system with reverse osmosis (RO) or nanofiltration (NF) elements is adapted to provide high recovery from difficult wastewater. The system has a plurality of stages. The system is configured to provide concentrate staging. The last stage also has concentrate recirculation. The valves and pumps of the system are arranged such that the order of flow and a recirculation pump may be switched between the first stage and the last stage at some times.