Mark says:Water will not soak through the rug itself but I would think water would get under it some through the zippers. The bedrug doesn't shift around like a solid plastic bed liner does so it won't rub through the paint leaving bare metal. As long as the paint is intact, the small amount of water that does get under the rug shouldn't cause any problems.
I got into the habit of taking the rug out at least once a year, washing the bed and applying a good coat of wax (NXT).