A fuel cell system including a compact, low-pressure-drop, high efficiency water-separator for separating liquid water from water-laden streams of the system. A cyclonic separator includes a sump for collecting the water, a drain for removing the water from the sump and directing it to a reservoir, a shutoff valve associated with the drain for controlling flow through from the drain, and a water level switch that controls the opening/closing of the valve. The switch triggers closing of the valve before the sump is emptied to provide a water seal that prevents escape of gas through the drain.