A flow shifting fuel cell with water separator. The water separator is used to control the amount of moisture that passes through the anode flowpath of one or more fuel cells in one or more fuel cell stacks. The water separator is made up of a housing to direct the flow of a moisture-bearing fluid as well as act as a collection and container for separated moisture. Fluid that is cyclically passing through the fuel cell stack as part of its flow shifting mode of operation oscillates back and forth across a separation chamber formed within the water separator, thereby allowing bidirectional control of the moisture content within the fluid. A drain is formed in the separation chamber to allow removal of condensed water.