I would think it would depend on the type of water spot. If the spot is some kind of residue sitting on the top of the glass, then you should be able to remove it. If the spot is the result of some kind of chemical reaction that has etched the surface of the glass, its a much more difficult repair. You would have to use something that could remove a significant amount of glass to make a smooth surface. Glass is way harder than paint and I have never seen this type of repair successfully done.