The simplest answer I can give you is you avoid for a week or two before topping up with them.
Normally, these tanks are sealed although I do not have the exact design in mind but I would believe they have backflow preventers on their pumps (meaning fuel should not go back after it has been "read" and that would go the same with water. It shouldn't be able to flow in through the pumps.
As for the manholes of the tank, I believe it is a double seal system that prevents the water from actually getting into the tank.
But even with these in mind, I avoid them after floods for about two weeks. At least that gives them time to check and maintain their tanks and equipment. But to say completely avoid them is quite hard if you live in a flood prone area though.
