These are likely not water spots, but an etch mark in the surface of the stone. This is what happens when an acidic substance comes in contact with any calcium based stone. To get rid of the etch marks, the stone will need to be polished out, much like a gemstone would have to be if it were scratched. If the etch mark is minor (i.e. you can see it, but can't really feel it with your finger) we recommend that you first try using a high quality Marble Polish. (See our  Caring For It page.) If the etching is more severe, you will need to have it professionally serviced. If this is the case, call us.