I had a similar situation on windshield and side glass on one of my cars. Using solft well water that, at one time, was "cleaner" than most "treated" city water. Yet the water spots persisted and nothing could really completely remove them. No glass cleaner would remove all of them, either.
I recently tried some Griot's Garage Water Spot Remover. Spray-on liquid I got at AZ. I sprayed it on, moved it around with a microfiber car wash wand/soap applicator, then followed it with "soap" (in this case, car wash soap, then rinse as specified) and not only were the water spots gone, it also cleaned the glass better than any glass cleaner I had ever used. Water spots are still gone a few months later, too.
It was cautioned to not let the remover dry, but it also seems to have an oil-base, which the soap is used to neutralize. I can say "It worked for me".
On the side windows, I followed it with RainX spray glass cleaner and that worked well, too.
JUST MY experiences,
CBODY67