Approaches currently used for remediating acid mine drainage (chiefly active chemical treatment and passive bioremediation systems) have a number of major detractions, including their failure to recover potentially valuable metals from these waters. Bioremediation strategies that utilize reactor-housed microorganisms can circumvent this problem, but have tended not to be widely used due to their relatively high costs. We have devised innovative approaches for remediating mine waters that use acidophilic bacteria to remove metals either as oxidized or reduced phases, using modular bioreactors that are designed to operate at minimal cost and to generate products that have commercial value. A composite system is described that combines microbial oxidation of ferrous iron with abiotic precipitation of ferric iron as schwertmannite, a mineral that has commercial value as an absorbent of arsenate and other environmental pollutants, and as a pigment. Sulfidogenic bioreactors maintained at acidic pH values are used to selectively precipitate metal sulfides, such as CuS. Tests with synthetic mine drainage containing mixtures of soluble metals confirmed that these systems can generate relatively pure mineral deposits from complex acid waters. The units are designed to be configured differently, according to the nature of the mine water requiring treatment.