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Manganese (Mn) is a metal similar to iron which causes grey/black staining. Manganese can cause staining in concentrations as low as 0.05 ppm. Manganese is removed in a manner similar to iron, although oxidation is more difficult, requiring a pH of at least 8.5.

Natural sources of manganese are more common in deeper wells where the water has been in contact with rock for a longer time. Manganese is readily apparent in drinking water supplies, causing a strong metallic taste to the water and causing staining. Water coming from wells and springs with high manganese may appear colorless initially but black (manganese) stains or particles quickly appear as the water is exposed to oxygen.