I moved the tank vent on my boat 9" higher after a similar problem on a windy day on Hood Canal.

I also changed out the gas tank filler cap from a cheap one that kept on cross threading and allowing water to get in the tank that way.

Finally, I added a fuel filter/water separator that has a drain basin with a petcock to remove excess water without changing the whole filter assembly.

These cost about $70 to complete all of the midifications, and I would suggest that you do all three before ripping up the flooring on your boat.