A few things to try from least abrasive to most abrasive.
Distilled white vinegar (let some dwell on your paint for 2-3 minutes, then rinse/dry, repeat a few times if necessary). I'd try this at full strength (i.e. don't mix with water). Do this in the shade, on cool paint. If the stain is etched in, this might not do much to improve things.
Do you have pro polish or AIO? If you do, try them (by hand) on a few spots to see if it improves things.
Sometimes you have to level stubborn water spots with compound -but that would be may last resort option as it's the most abrasive.
A few more options:
-Wet sanding (Have a pro do this if you don't know how).
-Paint De-con system. ABC and Finish Kare have chemical kits that claim to remove contaminates from your paint, including water spots.