Ask a Professional Cleaning Technician:
How do you remove hard water stains from toilet bowls, and how do you prevent them from building up in the first place?
First, flush the toilet so there is only fresh water in the toilet bowl, then put on your gloves.
Second, you want to lower the water in the bowl so you can work on the stain. You can do this one of two ways: Pour about a gallon of water into the bowl – this empties the toilet without refilling it. Or use your toilet brush and vigorously push the water into the drain. Neither method will totally remove water from the bowl but will lower it to the point where the hard water stain will be exposed to the chemicals you need to use to remove the hard water stain.
Third, apply a commercial product such as CLR (a calcium, lime and rust remover) to the stains with a sponge, scrub brush, or pumice stone and let sit for about two minutes., then flush the toilet. Repeat if necessary.
Fourth, scrub with a product like CLR about once per month to prevent stains from building up.