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I know its frustrating but she is 10 years old and seals, etc will need to be replaced. I have to replace my starboard side fish box seal this winter as if there is a torrential and sustainable downpour - it will fill up - I can tell that bad weather moved through the area just by looking at whether the boat is slightly listing :) I think a new seal (the large black one around the entire bilge OPENING) should solve your problem. I’m not referring to the seal on the underside of the hatch itself. This seal is more vulnerable to tears, rips and crimping – especially in the back/hinge area of the hatch (where the scuppers are) Yes there is always some water around the two scuppers “indents” behind the hatch. I have never had a problem with the bilge hatch/seal – any and all water came from the circular hatches or the rectangular hatch in the motor well.