I've scrubbed and used bleach, ammonia and a stone and the water stains won't come out
Lysol toilet bowl clean in the black squirt bottle with a Mr. Clean Magic Eraser was able to remove stains that bleach and pumice didn't budge in one of mine.
I've had good success with vinegar and baking soda in my toilet, but if that doesn't work, another option is to use Hydrogen Peroxide. Here's the method from the blog of another Hometalk member. Wishing you the best.
Kathy gave you some good advice. I have hard water, and the only thing that helps me is Lysol Lime and Rust cleaner.