Microbial communities play a significant role in the treatment of inorganic constituents at mine sites, often through direct metabolic reduction. Targeted quantitative polymerase chain reaction (qPCR) allows for quantitative monitoring of specific genes, whereas next-generation sequencing (NGS) can be used to provide comprehensive microbial community profiles that are used to monitor important metabolic functions. In this study, qPCR tests, NGS, and differential plating methods combined with genetic colony identification were used to detect and characterize microbial communities that reduced selenate (SeO42−) to selenite (SeO32−) or SeO32− to elemental selenium (Se). This combination of novel and classic molecular biological tools provided multiple lenses to view selenium metabolizing communities and can increase our ability to understand how microbiology impacts treatment processes for selenium.