A fuel cell system that selectively causes cathode input air to by-pass a water vapor transfer (WVT) device during high to low power transients. During normal stack operation, the cathode input air is sent through the WVT device to humidify the cathode input air for proper membrane humidification. For low power stack operation, where the cathode input airflow is reduced, which reduces the ability of the airflow to drive water out of the cathode flow channels, a by-pass valve is switched so the cathode inlet air by-passes the WVT device to reduce the cathode inlet humidification. In one embodiment, heaters at the ends of the stack are turned on during the low power condition to further reduce the accumulation of water in the end channels of the stack.