The invention generally relates to a method and apparatus for collecting condensate from process streams in an integrated fuel cell system. In one aspect, the invention provides a water management subsystem for a fuel cell system. A gas conduit contains a gas at a first pressure. A water tank in the system contains water at a certain level. The water tank has an inlet orifice below the water level. A drain conduit has a first end and a second end. The drain conduit is connected at the first end to the gas conduit, and the drain conduit is connected at the second end to the inlet orifice of the water tank. The water level and the inlet orifice have a vertical height of water between them corresponding to a head pressure greater than the first pressure.