The best way to remove a rust stain from a toilet is to use a toilet brush and a cleaning agent that contains diluted hydrochloric acid. Before cleaning the toilet, start with a dry bowl to prevent the cleaner from becoming diluted.
Before attempting to clean rust from a toilet bowl, close the water valve by turning it clockwise until it stops. To avoid causing harmful vapors, flush the toilet to remove any residue from previous cleaning products.
Plunge the toilet bowl to remove as much water as possible. When the bowl is relatively dry, pour a cleaning product containing hydrochloric acid onto the bristles of a stiff nylon toilet brush, and spread the cleaner throughout the bowl and over the jet openings. Scrub the stains until they are gone. If necessary, reapply the cleaner to the brush, and scrub again.
The label of a toilet cleaning product may list a hydrochloric acid ingredient as hydrogen chloride, muriatic acid or HCL. Never use a product containing bleach to clean a rust stain, as bleach can set the stain. It is also important to avoid using a wire brush, as this can scratch the bowl and make it hard to remove rust stains.