The amount of water produced as a byproduct from PEM fuel cells depends on how may stacks you're using.
The best way to condense the produced water vapor is to use some of the electricity generated from the PEM fuel cell stack to drive fan cooler to condense this water vapor.
The condensed water is not usually wasted, but put to some use. Condenser can be air cooled or water cooled. If your fuel cell can run at higher temperature the efficiency can be increased by using the condenser to warm up the incoming air, especially in cold weather.
In fact, the quantity of water depends on the number of stacks and their size. The develoment of suitable cooling system can condence the water vapours and that will be pure water.