A control strategy for bleeding an anode side of fuel cell stack in a fuel cell system that improves water management and addresses durability and performance concerns. The method includes determining when to begin the anode bleed, typically by estimating or measuring the amount of nitrogen in the anode side of the stack. The method also includes determining when to end the anode bleed based on the volume of gas that has been bled. The method determines the mole flow rate of the anode gas flowing through a bleed valve, integrates the mole flow rate to get the number of moles of the gas that have passed through the bleed valve, determines a desired amount of moles to be bled, and ends the bleed when the actual number of moles of the gas equals the desired number of moles of the gas.