The question should be, how did the water get in there in the first place, and how much ? It is possible it was not witerized properly, or not at all, and froze and cracked the head or cyls, or leaking head gasket.
Water is detrimental to crank bearings, hence the reason to act very quickly to a ski that has been submerged. You only have hours before rust forms on the bearings.
You have two options to get the water out. Pull the engine, tear it down and spit the cases and check the bearings, and check the head, cyls, and exhaust manifold for cracks, or run it very easy on the water at operating temperature for about 15 min (but I would refrain from this until further investion eliminates the possibility of cracked or leaking engine components).