Something similar happened to me last summer... I just drained the oil, started the engine for a few minutes, drained the oil again and kept doing it untill there was no more water in the oil. Did it about 4 or 5 times. Needless to say I used cheap oil in the process ;)
It is kind of hard to make the airbox water tight...If you want to play in deep water, buy a Sea-Doo!
If you really went deep, I would also take the carb off for a good cleaning, if there is any sand in it, it probably found its way to the cylinder and the crank bearings...Not good!