Leaking exhaust!?

Since ive purchased a 98' Moomba outback, ive noticed that it tends to take on more water then any boat ive had in the past. Making sure the auto bilge worked, I felt ok about it. I went out Friday night and docked the boat at about 10pm. I came back around 3pm the next day and the water was just above the floor level. I turned on the bilge and it pumped all the water out. I checked to make sure the water didn't get high enough to get into the oil pan. I was ok there. I started to boat up and it drove fine. Went immediately to the ramp and pulled it out. Drained to boat and took the doghouse off and the floorboard. Put the boat back in and let it sit. I didn't see any water leaking in anywhere from the naked eye. Once I started it up, I could see water coming in at the exhaust or the muffler tube on the starboard side. I think this is the problem but would that cause water to come in while the boat is off sitting in a protected marina with no waves? It looks as though the flaps have been replaced and seem to be kind of open all the time. It also looks as though another coupler or something has been put on it in the past.
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The rear of your port muffler has been repaired with fiberglass. You probably have the same problem on the other side. Grind it down and put new fiberglass on it. Paint it black if you care to have it match better. Not a hard job.

Thanks! Appreciate it. Ill get on that this weekend and let you know how she goes.