First thing - refill it with clean oil immediately. Any time it is left empty will let air get to the parts that were affected by water and they will rust. Keep it filled and sealed even if you use engine oil or whatever you have handy. Next thing is to replace the seals. Best to do them all at the same time. Drive shaft seal, prop shaft seal and can't remember if there is a shift shaft seal also, but probably is. When you have if stripped to do the seals, flush it out with some suitable solvent, let it dry, and then reassemble and refill. If you can get a pressure test done after doing the seals that would be worth doing also.
