You can remove toilet bowl rust using Shaw's Pad Toilet Ring Removers, pumice stone scouring sticks, ZUD or The Works toilet bowl cleaners or citric acid powder. The most environmentally friendly and chemical free cleaning options are the Shaw's Pad Toilet Ring Removers, pumice stone and citric acid powders.
About.com and FamilyHandyMan.com suggest that toilet bowl cleaners that contain diluted hydrochloric acid are generally the most effective even though they are not environmentally friendly. However, you should not clean toilets that are linked to a septic system using products with diluted hydrochloric acid as this kills the bacteria in the septic tank, which ruins the septic system's ability to break down waste.
Use pumice stone sticks and Shaw's Pad Toilet Ring Removers to scour the rust from the porcelain toilet bowl surface. You should apply cleaners that contain diluted hydrochloric acid using a nylon bristled brush to avoid scratching the surface of the toilet bowl. A scratched toilet bowl that has rusted over is extremely difficult to clean.
You should never use bleach to remove rust from a toilet bowl as it causes the rust stain to set, which makes it even more difficult to remove. Furthermore, you should never mix bleach with cleaners containing hydrochloric acid as the two chemicals can react to make a toxic vapor.