Sulfate-reducing permeable reactive zones (PRZs), such as anaerobic wetlands, sulfate-reducing bioreactors, and permeable reactive barriers, are an attractive means of passively treating mining influenced waters contaminated with heavy metals. While the low cost and maintenance requirements are significant advantages of PRZs, the lack of clear design criteria is a disadvantage. It is not known why some systems will function for long periods of time without need for intervention, while others fail or do not recover well when exposed to stresses such as winter weather or other changes in conditions. This study explores the role of microorganisms in PRZs and the potential to use selected inocula to improve performance with respect to start-up time, sulfate-reducing activity level, and activity retention time. We have compared these attributes using various inocula, including: dairy manure, anaerobic digester sludge, acclimated column inoculum, and inoculum collected from two sulfate-reducing bioreactors operated in the field (Luttrell and Peerless Jenny King). Our results demonstrate that there are clear differences between the inocula and that the Luttrell bioreactor inoculum performs the best in terms of start-up time and overall activity. Sulfate concentrations, metal concentrations, and pH were measured in the aqueous phase to evaluate the ability of the different inocula to remediate acid mine drainage (AMD). In subsequent studies, DNA-based methods that profile the microbial community will be used to determine what kinds of microorganisms are present and to quantify key functional groups, including sulfate reducers, methanogens, and cellulose degraders. The ultimate goal will be to transfer these results to the field by developing the capability to intelligently design inocula for site-specific concerns.