The weathering of coal mine waste rock releases iron, calcium, sulfate and associated trace elements like selenium (Se). Nitrogen species are also found in association with coal-mining drainages mainly due to the leaching of residual blasting compounds. Elevated concentrations of Se are a ubiquitous occurrence in coal-mining environments in British Columbia. A major concern with waterborne Se in British Columbia is the potential for its bioaccumulation in aquatic food chains. Treatment to remove Se from coal-mining waste waters has proven to be challenging for conventional water-treatment technologies. Compounding this challenge, many streams are characterized by high flows and low selenium concentrations. Conventional membrane and ion exchange treatments produce concentrated brine streams that are difficult to treat or require disposal. Conventional biotreatment systems use excess nutrients to provide the required electrons to compensate for inefficient and variable electron availability, as well as to adjust reactor chemistry. This paper’s electro-biochemical reactor (EBR) technology provides a controllable and consistent supply of useable electrons to the microbes directly at a low voltage potential (1–3 V) and low current. In this manner, the EBR technology overcomes the shortcomings found in conventional systems, as it reduces the required nutrient addition and provides a more controllable, efficient, economical and robust biotreatment system. Additionally, the EBR process does not produce excess solids or biomass; therefore, solids management post-treatment is not required. Laboratory EBR bench-scale and on-site pilot-scale systems were used to treat five British Columbia coal-mine waste waters; influent Se concentrations ranged from 35 µg/L to 531 µg/L. Se treatment targets for the tested waters ranged from 5 to 10 µg/L. Mean Se concentrations in EBR effluents ranged from 0.5 µg/L to 1.4 µg/L, while reducing sulfate concentrations. The test data demonstrate that the EBR technology is an effective Se removal option for British Columbia’s coal-mining waste waters.