When I went on a charter in Florida, the captain put plugs in the scupper drains on the boat deck when we stopped to fish. This was a bay boat, and if the plugs weren't installed, the deck would get water on it as the scuppers must have been right at the waterline. Just an idea, but maybe using plugs on the inside of the boat while fishing would keep the water off the deck, just be sure to remove them when appropriate.