Some good advice in here, also some not so good advice in here. Then theres also some REALLY bad advice that no one should listen to. LOL
A lot of the things mentioned will work so long as the spots are truly surface spots and have not physically etched the glass. There is a difference between a water spot and water etching -
A water spot is the minerals or whatever was in the water (pollutants, dust, pollen) left behind once the water evaporates. It sits on the surface of the glass and if you could get it under a microscope would just look like some crusty film. Options for removing water spots (in order of least to most aggressive) -
- Wash and dry the vehicle
- Glass Cleaner with a glass cleanign towel
- 1:1 mixture of vinegar
- Clay bar + glass cleaner
- Bon Ami or similar abrasive cleaners
- Automotive cutting compound + cutting pad on a machine
- 0000 steel wool with glass cleaner
Now if you've tried all those and you find the spots are not improving or removed you are likely dealing with etching. Etching is the nasty big brother of water spots... basically a water spot that had the right conditions to physically damage the surface and somewhat 'eat' into the glass. A combination of acidic rain, contaminents already on the surface, a lack of protection, heat, sun, and time all go into turning water spots into water etching. No amount of cleaners or scrubbing is going to fix etching, you have to level the glass.
In the OP's case it makes sense that it might be etching as water sitting on the sunroof is going to get more heat/sun exposure and the water will sit for longer versus side windows - thus the reason it wasn't a problem on the sides, but is on the top.
The sure fire way is the use of an actual glass cutting polish. Its messy, its nasty, but it will take a few mils off the surface of the glass and get you back down to a smooth un-etched surface.
Most effective glass compounds are going to be a liquid called cerrium oxide and they're designed to be used with a rotary polisher and bronze wool (yes, metal bronze wool) buffing pad. It casts off an ugly black liquid everywhere, makes a huge mess, but I have yet to encounter the glass I can't fix with that combo, including the 10 year old shower doors in the last house we purchased as a foreclosure.
There should be shops local to almost anyone that can do the service. If you're brave enough to take it on yourself I'd recommend this kit -
Amazon.com: Diamond Clear Glass Renewal Treatment: Automotive