distilled white vinegar wipe it on the window works great for light water spot and for stubborn water spot try powdered cleanser on a wet sponge rub away and rinse with water. (I use comet or Ajax No scratch Cleanser )..
Are they above-surface spots (deposits) or below-surface spots (etching)?
Spots sitting on the glass surface can be polished off with a cleaner wax, a dedicated glass polish, or try STANG5's suggestion and use white vinegar to dissolve the deposits.
Spots that have etched into the glass take more specialized skills. Maybe a auto glass professional can advise.
If it's caused by mineral deposits, most acid-based cleaners (such as CLR) works well, so long as you don't drip it onto your paint.
If it's caused by some other things (e.g. industrial fallout, silicone deposits from synthetic wax/armerall), you may have to get something to strip it out. There are some car windshield wax strippers available and I personally know a couple of them but unfortunately, one of them can only be available from the Orient (by Soft-99).
Get some Duragloss Nu Glass. Best glass polish/cleaner Ive used and its not expensive. Took off years of acid rain spots, etc etc etc.Check Carquest, if they don't stock it they can get it for you quickly or order it from Autogeek.
You can try taking a razor with some lube like soapy water. Scrape the glass with the razor. Thats how we used to prep glass for Window tinting. The razor will remove everything and anything that is on the surface.