Selenium is a widespread contaminant released by industrial activities such as coal combustion. In selenium-contaminated groundwater, native microbial communities commonly have the capability of reducing the toxic oxyanions selenate and selenite to insoluble elemental selenium. The impact of local hydrogeography on microbial selenium reduction was tested by constructing laboratory microcosms using biofilm and groundwater collected from four monitoring wells screened in three distinct stratigraphic units near fly ash disposal ponds in southeastern Montana. Glycerol, methanol and molasses were tested as carbon amendments. Nitrate and selenium concentrations were monitored, and microbial communities were sequenced to examine differences among sites and carbon amendments. All site and carbon combinations resulted in nitrate removal, though molasses had the highest removal rate. Selenium removal was significantly impacted by stratigraphic unit, with microcosms from alluvial wells removing more total selenium than those from coal and interburden wells. Microbial community composition was correlated with site, carbon amendment, and nitrate and selenium removal. Furthermore, two genera from the order Clostridiales, Desulfosporosinus and Gracilibacter, emerged as potential indicator organisms for selenium reduction in this environment. The site, carbon amendment, and microbial community were all found to potentially impact remediation efficacy.