Mike.Mike I don't know if you meant water spots on your entire car or just the windows and I don't know if you meant like the little residual spots or actual waterspot etching but for the former, you can try a paint cleaner or similar(good for both the windows and painted surfaces) but the latter(the etching) would typically require a polish. Softer paints in hard water areas or industrial areas are prone to bad etching.
One double edged sword though, keeping your paint and glass protected from etching compared to nothing. Quality waxes and sealants make water bead really well but if youre not there to rinse and dry it and the water dries, you end up with nice round water spots(though typically residual as opposed to the actual etching) lol.
I say keep it protected and take the water spots in stride...If it makes you feel any better I constantly clean my windows.