If you have water on the tops of your pistons more than likely the entire bottom end is full of water too. If you live in a cold climate (freezing temps) might have other problems ie cracked block. did you roll your ski? water just doesnt go in there, you got and issue with your motor, wheter it be a roll over, cracked block, water geting in the cylinders around the head.
Depending on how long the waters be in there, Id say you going to have compression issues, pitted cylinder walls, crank issues, from the rust. I dont know the full story but to me sould like your going to be rebuilding.