Well first make sure it is in fact whats happening! Easiest way is to duplicate the problem & be prepared to pull the spark plugs, then crank it to get rid of the water.
If it does infact happen, replace your water shutters. Their in the exhaust system, allow exhaust past them but won't let water from the other direction.
What style manifolds do you have? Log (long w/riser at the back), or center riser ( with riser in center).