Deep drains used to manage shallow saline water tables in the Western Australian agricultural region discharge acidic, saline drainage water with high concentrations of metals. The activity of sulfate-reducing bacteria can treat these waters by generating alkalinity in the form of bicarbonate and by generating sulfide, which removes metals from solution as sulfide precipitates. Bacterial sulfate reduction was strongly influenced by the organic carbon substrate provided for bacterial consumption. Mixtures of lupin compost, wheat chaff, oil mallee distillate wastes, straw, ethanol, and sheep manure were compared to determine which substrate was most effective in promoting the activity of sulfate-reducing bacteria and the contribution of this to bioremediation of acidic saline drainage. Mesocosm treatment systems containing reactive mixtures and acidic saline drainage were operated for a 50-day establishment period and subsequent 27-day “batch flow” period. Effluent from the treatment systems was analyzed for pH, sulfate, metals, and nutrients over the period of operation. Effluents from all reactive mixtures showed increased pH (to 5.1–5.9) and decreased sulfate and metal concentrations compared with untreated drainage water. Straw with ethanol appeared to be the most effective substrate for treatment of low pH and high metal concentrations, followed equally by both lupin compost and wheat chaff. The latter are likely to be more suitable for use in a field scale low-maintenance bioreactor or composting wetland.