Acid mine drainage (AMD) from abandoned mines cause environmental harm and requires cost-effective, passive remediation techniques. Mining activities expose mineral surfaces to oxidation, which accelerates the release and mobilization of acidity, sulfate, and metal ions in AMD. Sulfate-reducing bioreactors (SRBRs) are an attractive means to treat AMD by reducing sulfate, increasing pH, and precipitating metals as metal sulfides. Twelve SRBRs were constructed and operated for 12 months to evaluate AMD bioremediation performance as a function of carbon source and inoculum. Several locally-sourced waste organic materials were characterized by carbon fractionation; two mixtures with the same carbon profile but originating from different sources were used as organic substrates. Microbial communities from two different soil types were used to inoculate the bioreactors. The use of cow manure, corncob, and pinewood as the carbon source and soil from a local pond shore as the inoculum resulted in the greatest bioremediation efficiency, with a pH increase from 2.85 to 6.80 and removals of >82% for total Fe2+, >86% for Cu2+, >88% for Zn2+, and >65% for SO42-. The source of inoculum was found to impact bioremediation startup, with sulfate reduction observed 20 days earlier in high-performing inocula. The carbon source was found to impact long-term bioremediation efficiency, with 24% more SO42− and 38% more Fe2+ removed by the best performing carbon sources. Altogether, the combination of manure as a carbon source and marina soil as an inoculum resulted in the highest bioremediation efficiency. The high metal and sulfate removals combined with pH increases to near neutral, validate the use of SRBRs as an effective method for long-term AMD bioremediation.