Homeowners who draw their water from a well may find black stains in their bathroom bowls due to particular elements dissolved in the underground aquifers that provide the well with its water. The dissolved elements aren’t considered a threat to health despite the fact that they may stain plumbing fixtures or impart an unpleasant taste or smell to the water.
Iron and manganese dissolved in well water are the principal culprits behind dark stains in toilets and about other plumbing fixtures. Iron is the worst stain maker. Since the water sits at the toilet bowl, the dissolved iron and manganese mix with oxygen from the atmosphere to form dark oxide chemicals which settle out of the water and onto the toilet bowl.
To get rid of black bathroom stains, switch off the water, flush the toilet and plunge just as much water as possible out of the bowl. Coat the stains using a liquid toilet bowl cleaner containing dilute hydrochloric acid, also known as muriatic acid or hydrogen peroxide. The cleaner quickly reacts to loosen the stain. Scrub off the stain using a nylon-bristle bathroom brush. Work slowly to prevent spattering. Turn on the water and flush the toilet. Never mixture acid-based bowl cleaners with bleach-based cleaners; they react chemically to release lethal chlorine gas.