The removal of sulfate derived from mine impacted waters is a major objective when treatment is focused on removing potentially toxic metals and metalloids, and neutralizing the acidity of these polluting waters. Here we report on the use of a mixed culture fixed-film column bioreactor including one acidophilic sulfidogen operated for 270 days to primarily remove sulfate from an acidic synthetic water that contained a low level of zinc (0.15 mM). Changing the hydraulic retention time (HRT) from 100 to 30 h caused minor perturbations in the removal of sulfate (∼40%) using 6 mM of glycerol as carbon and electron source; however, lowering the HRT to 25 h did not sustain biosulfidogenesis. By increasing the concentration of glycerol as electron donor to catalyze the dissimilatory reduction of sulfate, it was possible to reduce the concentration of sulfate from 14 mM to ∼3 mM. This corresponded to an ∼80% removal efficiency from the acidic water feedstock, which is well below the lowest attainable concentration using conventional technologies such as gypsum precipitation. Molecular analyses of the column effluent demonstrated that the mixed culture population changed with varying concentrations of glycerol, highlighting a role for Clostridium sp. in the degradation (removal) of acetate produced in the bioreactor by Desulfosporosinus acididurans.