No matter how good you think the seals are, water will get in. I never figured out where but my boat will get water in it if it rains hard. Everything is closed up and, in theory, sealed. Hatches to get to the bilge pump, live well pump the hatches for the rear seats, around the big hatch in the center of the boat for the gas tank and sending unit and wiring harness. They all have rubber seals and I am sure that eventually, they all leak a bit.
It's not a big deal. What I usually do is as I come out of the cove, I'll bring the boat up to about 3K RPMs. They will point the hull up and whatever water is inside will drain back. I will have the bilge pump on and it will usually pump out about 5 to 10 seconds of water. No biggie!
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