Ah. If I was concerned that there was a good possibility of running through water high enough to submerge my air filter, I'd run a short ram, and keep the filter up in the engine compartment.
You know, there is just (and I mean JUST) enough room inside the back of the fender to put a small cone filter in there, or maybe one of those longer oval K&N's. It would require some cutting and fabing(I think you'd have to move one fender bracket in there), but it would make a nice place to run a short cold air intake system. You'd have to vent the fender to get enough air, though.