Soluble manganese (Mn(II)) can cause nuisance and occasionally toxicity problems, both in surface and ground waters and in domestic water supplies. Many mine drainage waters contain highly elevated concentrations (often >100 mg l-1). Current systems for remediating mine waters, although effective for other metals, are often inefficient at removing manganese. This paper describes the development of self-sustaining, low-cost bioreactors that can be used in situ for passive removal of manganese from mine waters and other contaminated water courses of pH >4. A prototype bioreactor, set-up using Mn(IV)-coated pebbles from a fresh-water stream, was tested over one year and shown to be effective in removing Mn(II) from 10 to <0.25 mg l-1. Two species of fungi and one bacterial species were isolated from this system as Mn(II)-oxidizers. The fungi were identified as belonging to the order Pleosporales (Ascomycetes), and one was related (98 % 18S rRNA gene sequence identity) to a known Mn(II)-oxidising fungus. The bacterial isolate was closely related to the α-proteobacterium, Bosea thiooxidans. T-RFLP analysis showed that one or both of the fungal isolates were the dominant eukaryotes in the bioreactor community.