The invention generally relates to a method and apparatus for collecting condensate from combustible gas process streams in an integrated fuel cell system. In one aspect, a water management subsystem for a fuel cell system has a first conduit containing a first gas at a first pressure. A first water trap is provided that is configured to receive condensate from the first conduit. A second conduit is provided that contains a second gas at a second pressure. A second water trap is provided that is configured to receive condensate from the second conduit and the first water trap.