Simple – get them off as quick as possible. Spray-on paint products like Mothers Waterless Wash & Wax or Instant Detailer are ideal for this purpose. Keep detailer and a clean terrycloth or microfiber towel in your sled at all times, because when you’ve got to remove the worst water spotting, you’ve got to do it ASAP (the faster you get to it, the less time the chemicals in the “spot” have to etch the finish). In addition, don’t let the sun bake those water spots, or they’ll be even tougher to remove. Detailing spray also works great to save your finish around the fuel door, in case you spill gas while refueling.
If water spots have been around for awhile, work them with a polish – like the one found in Mothers Scratch Remover. Follow up with a traditional wax in order to ensure the paint is properly protected.