Before resorting to a heavy rubbing compound, I'd try something with a lighter grit, maybe a polishing compound such as one made for boats by 3M, and available at WalMart. IIRC Maguires makes a similar product. You can always go to the harsher grit rubbing compound if you need to.
I'm just curious if/how you know these are water spots vs the natural oxidation that happens to gel coat. We get lots of "spots" on our boat that that are actually bird poop, and they really stain gel coat.
FWIW I practice prevention from water spots; I towel dry our boat after washing it. The whole process takes me 6 hours each time, but I don't get any water spots remaining. One of these days I'll cough up the $$ to install appropriate filters at our dock, although I suspect it won't totally eliminate the towel drying.