Hi Whiskey,
Water spotting or marking is mostly a problem of "Hard" water which contains minerals, salts, calcium,and lime residues that have baked, and etched into the glass.
There are professional glass cleaning and scratch removal companies out there that would remedy your problem. Being in the auto spraypainting game, i have used 2 Pak cutting compound and a buffing/polishing machine in conjunction with a foam or lambswool buff pad and have achieved excellent results in removing the staining. You can use the compound without a buff, but obviously, it will take a lot of elbow grease and effort to get the desired results.Your glass will never be scratched or damaged when using these 2 pak cutting compound products.
A word of caution when using steel wool of any description.(I never use it at all). The problem is that when you use steel wool for whatever reason around any paintwork, the wool sheds thousands of very tiny sized fibres as you go about using it. It is absolutely imperitive to totally remove all the residue fibres from surrounding paintwork areas. If you don't, the fibres will rust. If rusted fibres are left on the paint surface, they etch or literally weld themselves onto the paint surface, and are very, very hard to remove from that painted surface. So much so, that in some cases, you are forced to refinish the panel that has been affected. I've run into that problem several times over the years, and for that reason, won't use the stuff at all.
There are other types of polish/abrasive poducts out there that do just as good a job or if not better than the old steel wool.
Hope that helps,
Greg