If you get water spots, its usually either dirt,salt or minerals in the drops.When the water drys, the dirt/salt/minerals are left.
There are a few ways to get rid of them.
1. Soapy water will usually do the trick.
2. A spray cleaner like windex can also work. The small amount of alcohol will remove the spots usually (just like on your windows).
3. If the spots are more tenacious, you can add a little vinegar to some warm water and rub with a soft cloth.
4. Last resort would be car polish/wax that you would use to make old paint look new again.
With all of the above, use a soft cloth to avoid scratching you paint.