Sounds to me like those spots/stains have etched themselves into the clear coat. Buffing sounds like your only fix. If you are not confident doing it yourself have a professional detailing shop do it. Very easy to burn through the clear coat if you don't know what you are doing. Once it gets clean, my suggestions work. Todk64 mentioned the Mother's Chrome Polish...good stuff just might help. I've used it on other things and the stuff is amazing. Don't know how it will work on your water spots.

Pat