A cell stack assembly (102) coolant system comprises a coolant exhaust conduit (110) in fluid communication with a coolant exhaust manifold (108) and a coolant pump (112). A coolant inlet conduit (120) enables transportation of the coolant to the coolant inlet manifold. The coolant system further includes a bypass conduit (132) in fluid communication with the coolant exhaust manifold and the coolant inlet manifold, while a bleed valve (130) is in fluid communication with the coolant exhaust conduit and a source of gas. Operation of the bleed valve enables venting of the coolant from the coolant channels, and through a shut down conduit (124). An increased pressure differential between the coolant and reactant gases forces water out of the pores in the electrode substrates (107,109). An ejector (250) prevents air form inhibiting the pump. Pulsed air is blown (238,239,243,245) through the coolant channels to remove more water.