Not all well water stains toilet tanks and bowls black. Only unfiltered or untreated wells that contain manganese in the water leave black stains in toilets, in the laundry and even on clothes. Well water with manganese in it most likely also contains iron, sulfides, calcium and magnesium, all of which do not present health hazards, but can leave toilets, tubs and laundry stained and smelly.
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Manganese in well water comes from the rocks and minerals deep underground through which the water passes. If the well's piping is iron or steel, it can also be the cause of manganese in well water. Manganese staining can start out dark brown, but with time, it builds up to a black slime inside the toilets, pipes and fixtures. If left untreated, it can build up inside well systems, pressure tanks and water heaters, or serve as a host to a variety of bacteria that feed on its soluble forms. Cleaning the toilets won't fix the problem, as it will just return. And using household bleach can make the stains worse.
A licensed water treatment professional can conduct water tests to determine the parts per million of the manganese in the water, which helps him figure out the best method to treat the problem. Treatment options include various types of rock and sand filtration, injection treatment or a chlorination and oxidation treatment.