Chemical passive treatment systems used to remediate acid mine drainage has been evaluated based mainly on the reactivity of the chemical alkaline reagents, overlooking the activity of the microorganisms that proliferate in these artificial ecosystems. In this study, the bacterial communities of a unique passive treatment system known as BDAS (Barium carbonate Dispersed Alkaline Substrate) were investigated using 16S rRNA gene metagenomic sequencing combined with hydrochemical characterization of the AMD and phenotypic characterization of biogenic precipitates. According to the hydrochemical characterization, the water quality improved as the water progressed through the system, with a drastic increase in the pH (up to alkaline conditions) and total organic carbon, as well as the removal of main contaminants such as Ca2+, SO42−, Fe3+, Al3+, and Mn2+. These environmental changes resulted in an increase in bacterial diversity (richness) after the inlet and in the shift of the bacterial communities from chemoautotrophs (e.g., Ferrovum and Acidiphilum) to chemoheterotrophs (e.g., Brevundimonas and Geobacter). Some of these taxa harbour potential to immobilize metals, aiding in the treatment of the water. One of the mechanisms involved in the immobilization of metals is microbially induced calcium carbonate precipitation, which seems to occur spontaneously in BDAS. The production of biofilm was also observed in most parts of the system, except in the inlet, helping with the removal of metals. However, in the long run, the build-up of biofilm and precipitation of metals could clog (i.e., biofouling) the pores of the matrix, reducing the treatment efficiency. Potential human pathogens (e.g. Legionella) were also detected in BDAS indicating the need for a treatment step at the end of the system to remove pathogenic microorganisms. These findings present a new perspective of the bacterial communities and their effects (both positively and negatively) in a chemical passive treatment system.