The application of microbial consortia to remediate thiocyanate contamination at mine sites is an evolving biotechnology. This relatively persistent compound is formed during gold ore processing and can result in groundwater contamination by mine tailings. Previous research has focused on laboratory cultures, and there is a lack of knowledge about microbial communities and their metabolic processes in scaled-up bioreactors. This study applied genome-resolved metagenomic analyses to identify the key thiocyanate-degrading microorganisms in a pilot-scale (1000L), flow-through, moving bed bioreactor operating at a mine site in Victoria, Australia. Genome-based prediction was applied to explore potential metabolic interactions among microbial community members in this autotrophic system. Results highlighted the dominance of thiobacilli for thiocyanate biodegradation. Abundance analyses suggest a positive effect of attached growth in the bioreactor for proliferation of thiocyanate-degrading and ammonia-oxidizing bacteria. The relatively lower abundance of the latter group points toward the potential for ammonium accumulation and subsequently inhibition of thiocyanate biodegradation. We show here that thiocyanate bioremediation strategies can benefit from microbial strain variability and functional redundancy. Also, the role of nitrifying microorganisms should not be neglected if complete nitrogen removal is required.