Check the rear of the boat just above the ladder. The gap between were the top mold and the bottom mold of the boat come together. You will probably have to take the molding off to see it. When it's in the water look for bubbles. Most of the time this area is above the water especially when the boat is moving but when it's not moving and waves push up to he area water enters. If this is the problem just go get some marine grade caulk and caulk as much of the gap as needed and fasten the molding back in place.
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