Environmental contamination caused by oxyanions like nitrate, selenate, chromate, and other related functional groups in water and wastewater is identified as a serious threat to human health. Among the different techniques attempted to remove or convert these compounds, reduction with the use of microorganisms has gained importance due to high selectivity and efficiency. Hydrogen-based membrane bioreactor (HMBR) is identified as a suitable method due to the non-toxic properties of hydrogen as an electron-donor, reduced secondary pollution, and easy generation of hydrogen through cost-effective novel methods. This research article is focused on the principle and mechanism of removal of anions, organic compounds, heavy toxic polyatomic metal ions, and antibiotics using hydrogen mediated microbial reduction process. Denitrification studies in HMBR at different operating conditions, namely membrane type, pH, nitrate concentration, and hydrogen partial pressure, are reviewed and the commonly reported efficiency ranges between 70 and 100%. The removal efficiencies attained by HMBR are as follows: perchlorate 30-100%, selenate 92-100%, phenol 87-99%, arsenate 60-68% and halogenoalkanes 45-99%. The mechanism of reduction in HMBR was explained with reference to nitrate, arsenate, chlorophenol, and chromate.(c) 2021 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.