The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen, and mitigate sulfide oxidation. The cover system includes a vegetated, uppermost soil layer, underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste-rock capillary-break layer, installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were characterized by high sulfur and low carbon content. The bulk pH of the tailings pore water was circum-neutral (∼5.5 to 7.3). Total genomic DNA was extracted from 36 samples recovered from the constituent layers of the cover system and the underlying tailings, and was analysed in triplicates using high-throughput amplicon sequencing of the 16S rRNA gene. Iron-oxidizing, sulfur-oxidizing, sulfate-reducing, and aerobic heterotrophic microorganisms were enumerated using most probable number enumeration, which identified heterotrophs as the most numerous group of culturable microorganisms throughout the depth profile. Low relative abundances and viable counts of microorganisms that catalyze transformations of iron and sulfur in the covered tailings, compared to previous studies on unreclaimed tailings, indicate that sulfide oxidation rates have decreased due to the presence of the GCL. Characterization of the microbial community can provide a sensitive indicator for assessing the performance of remediation systems.IMPORTANCEMining activities are accompanied by significant environmental and financial liabilities, including the release of acid mine drainage (AMD). AMD is caused by accelerated chemical and biological oxidation of sulfide minerals in mine wastes, and is characterized by low pH and high concentrations of sulfate and metal(loid)s. Microorganisms assume important roles in the catalysis of redox reactions. Our research elucidates linkages among the biogeochemistry of mine wastes and remediation systems, and microbial community and activity. This study assesses the performance and utility of geosynthetic clay liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system.