Pull your fuel pump and disassemble it. There's a thread on here somewhere, I believe, on what to look for while in there.
There are two small rubber, spring loaded valves in it that need to seat. One on the intake side of the pump, the other on the outlet side. If the small rubber diddie gets loose from the spring, the pump won't keep up good pressure. If both get loose, the pump will lose all pressure.
Could be you are suffering from this type pump problem.
Water in the lines would pressurize the same as gas and you wouldn't hear the pump straining to maintain pressure.
Also, if when the bike warms up, you have a carb needle/seat not closing for some reason, that carb(s) will suck way too much fuel and maybe cause the pump to work extra trying to maintain pressure, also causing that carb(s) to flood over and kill the bike.
Start with the pump. It is relatively simple to get to under the seat, and easy to disassemble and inspect.