Rust is not your problem.
The main one is water does not compress. If it makes the combustion chamber then you will be luck if it lives.
The weakest component will go and without trying it not sure what will happen. But I have seen Spark plugs blown out, Head gaskets blown out, crankshafts bent.
As said above switch it off before it swallows any water. then make sure you empty the water out and remove the spark plug you may be able to turn it over with the key to get any out but I would start by laying the bike on its side (Once you have pulled it out the river) to drain as mush out as possible.
But best of all dont drop it.....
