I recently patched a possible hole in the bottom of my tandem wherry. With the advice of Laszlo (Thanks again!), i sanded, epoxied, glassed, primed and painted and it looks as good as new. I also took the opportunity to install an inspection port at either end and took the wherry out for a couple of outings this weekend. Unfortunately i found water in the forward air-tight compartment. I have had a good look and there is nowhere obvious where the water could get in. There is not a lot and i don't mind mopping it up, but if i just leave it, am i causing serious long term damage to the boat?
You may try putting a drop light in the compartment and check around the outside to see if any light shows.