This seal is there mainly to help keep fumes from engine compartment from getting past the firewall, and allowing them to be sucked into the heater blower motor and into the car.
Swimming pool huh. Make sure the drain holes and their rubber flappers (if still there) are open and clear on both sides of the cars cowling area. If your constantly parking your car on an incline (nose up) you will get some water collecting back there, but it should drain out soon after car gets driven and or leveled out again.
