Mine drainage waters often contain elevated concentrations of toxic metals and can be a source of environmental pollution. Manganese (Mn)-oxidizing bacteria (MnOB), which can oxidize soluble Mn(II) to insoluble Mn(III, IV) under neutral pH conditions, are expected to be a promising biological agent in passive mine drainage remediation. However, the diversity, functionality and applicability of MnOB for mine drainage treatment remain mostly unknown. Given that many mine environments are poor in organic substances, it is necessary to elucidate the functions of MnOB communities that contribute to metal removal without supplementation with extra organic matter. Here, we constructed in situ continuous-flow bioreactors for treating mine drainage containing approximately 20 mg L−1 Mn(II) and 6 mg L−1 zinc (Zn) (II) and operated these bioreactors without amended organic matter. The removal of Mn(II) and Zn(II) ions reached more than 98 % at a hydraulic retention time of 0.5 days. The X-ray diffraction pattern of Mn oxides deposited on the surface of limestone carriers indicated woodruffite-like mineral accumulation in the reactors. Several heterotrophic MnOB were isolated from the bioreactor, and metagenomic analysis revealed a predominance of diverse lineages of heterotrophs, including Elusimicrobiota, which harbored MoxA-like multicopper oxidase genes. Furthermore, the metagenomic analysis also suggested the involvement of gammaproteobacterial species that possessed putative genes for extracellular electron uptake and CO2 fixation. Our findings offer the first insights into the potential for chemolithoautotrophic Mn(II) oxidation processes via electron transfer from Mn(II/III) and application of chemolithoautotrophic and heterotrophic MnOB in mine drainage remediation without supplying organic materials.