Jet Ski has leak and engine compartment filled with water. Now wont start?

I have a kawasaki 1100 stxdi from 2002. I had a leak out on the water coming from the area where the impeller meets the hull on the bottom. Also, my engine compartment filled with water and my engine stalled. i hope water did not get into my engine and it was just my battery that shorted because of all the water. Im not sure what to do, any ideas??