OK... I just posted my response, and 2 above popped up. (strange)
Anyway... if you have water sitting in the engine... that's bad. It's a self draining engine.
With the plugs out... crank it dry. Then shoot in A LOT of fogging oil. (spark plug holes and in the intake) Then turn it by hand to distribute. (Then repeat) You want to make sure to realy get some oil into the engine. Then, I would remove the spin on fuel filter, and pour and ounce or two of your oil into that. Then start it, and just let it idle for 20~30 seconds, and shut it off. DO NOT run it on the hose. We want it to get a little hot to boil the water out. After it cools... do it again. We want that extra oil to just flood the engine.
Once this is done... you should be safe. But we need to figure out why it happened in the first place. Since it's self draining... it sounds like cooling ports may be plugged up. Did you find the water while it was on the trailer, or is it sitting in the water now?