Abstract: A system and method for removing contaminants from water that has a relatively low oxygen content with naturally occurring chemoautotrophic bacteria, ferrous iron, manganese, sulfide, and other contaminants. The system comprises an oxygenation vessel for oxygenating the water and a filtration vessel having bio-filtration media with surfaces that are exposed to the oxygenated water. The chemoautotrophic bacteria propagate in the presence of the oxygenated water and deposit certain of the contaminants on the bio-filtration media as by-products. The contaminants are also precipitated in the presence of the oxygenated water and settle on the bio-filtration media in at least the filtration vessel. A secondary filtration stage can further remove contaminants from the water that were not sufficiently removed by the first filtration stage.