I don't know your set-up, but you may want to consider adding additional amps. On my first boat, we had a 5 channel powering 4 tower (extended pylon actually) speakers and a sub, with the deck driving the speakers in the boat. I had the same issue, the amp would start shutting down within 30 minutes of getting on the water.
On the current boat, we've got one amp for the six tower speakers (800 watts), one for the interior speakers (600 watts), and one for the sub (600 watts). I'm still jonesing for more sometimes!!!