On Aliza we have the riser that Brian is recommending + the flap that SG wrote about. I have had a number of problems with water in the engine so I added the ultimate solution => a valve on the exhaust water trap tha drains into the bilge.

This way on a long sail when I shut the engine I can empty the water trap into the bilge and use the bilge pump to get the water out. If any water gets into the engine be from the aft exhaust or from the intake of the cooling raw water (due to a bad valve on the siphon break) it will only get into the bilge and pumped out with the automatic bilge pump and not get into the engine.