This can be a real problem. In 1987, I bought a pretty nice '67 Corvette coupe that was completely covered with water spots. I tried everything I could think of to try to remove them, to no avail. When I went to a pro, he said this is what can happen when a car sits with water spots out in the bright sun.
I ended up having it stripped and repainted. (I hated doing it, because for all intents and purposes, it was the original paint.)