Biological acid mine drainage treatment depends significantly on inoculum origin, pH, COD/sulfate ratio, and carbon source. In this study, the performance and microbial diversity of anaerobic batch reactors used for sulfate reduction was evaluated. A medium COD/sulfate ratio of 1.14 ± 0.10 was used, and the evaluation was performed in two steps: Phase 1, based on the inoculum source (autochthonous, AUT, and non-autochthonous, N-AUT); and Phase 2, based on the carbon source (lactate, ethanol, and formate) and low pH. In Phase 1, the sulfate removal using both AUT and N-AUT biomasses were similar, 53% and 59%, respectively. In Phase 2, ethanol and lactate as electron donors yielded similar sulfate removal efficiencies of 42% and 44%, respectively, at neutral pH. When the initial pH was reduced from 4 to 3, sulfate removal using formate remained nearly constant at 34%, whereas it reduced from 43% to 30% with lactate, and dropped significantly from 18% to 7% with ethanol. Denaturing gradient gel electrophoresis analyses for sulfate-reducing bacteria revealed their presence in all samples. Microbial activity and sulfate removal obtained for AUT cultures indicated that they possess the potential for use in local acid mine drainage decontamination processes.