Jetski's get submerged sometimes, with water in the engine.
The standard advice I've seen given is: pull the plugs and crank it over until no more water comes out. Then do whatever it takes to get it started (starting fluid, etc). Then run it hard for at least a half hour before turning it off. Its got to get hot enough to get all the moisture burned off from the inside of the block before anything can rust.
If they drain the water then let it sits a while, the bearings will rust and its doomed.