Some boxes are waterproof. I've never shelled out enough money to buy one (I just can't bring myself to spend $30 on a fly box), but that would be the way to go if you had to have one that was waterproof. My solution has been that I can't remember the last time I stood in water deeper than my waste in a river. I don't trust currents and slippery rocks enough. And another reason is that water that deep on tailwaters is usually doing one of two things 1. being generated (dangerous for sure) or 2. a long deep slow pool which isn't the type of water I like to fish. I'm much more particular to shallow riffles and shallow to moderately deep runs. Requires a lot more casting to fish quicker water but I get a lot of excitement out of seeing my indicator stop suddenly from a fast drift and beginning the fight. The hit and hookup are my favorite aspects of fly fishing. Except maybe when a hooked fish makes a run like a greyhound on a rabbit.
"I've got to stop wishin, I've got to go fishin"