there are a couple of areas where the water could be coming in. I think it would be best to just back it into the water without taking it off the trailer. You should be able to get a good idea where the water is coming in by doing so.
First check without the engine running to see if it's leaking. If not, fire it off and check it all again.
BTW, you'd be surprised how fast water will get in even with the smallest of leaks.