During the process of managed aquifer recharge (MAR), when the aerobic surface water is recharged into the reductive aquifer, the redox environment changes along the water pathway. MAR practice can reshape the initial groundwater bacterial community, and further induce variations in the bacteria-mediated hydrochemical reactions. In this study, laboratory-scale column experiments were conducted to simulate the processes of aerobic/anaerobic recharge to aquifer. The results showed that the concentration of DO during the aerobic recharge was higher than that of the anaerobic recharge, and ORP showed a similar trend. Active nitrogen transformation was observed during the simulated MAR processes. In the early stages of both the aerobic and anaerobic recharges, nitrate reduction occurred due to denitrification and DNRA. However, in the late stages, nitrification might happen in the aerobic column, and nitrate reduction remained the major process in the anaerobic column. For the bacterial community, Massilia, Ralstonia, Legionella, and Curvibacter predominated under the aerobic recharge. Comparatively, Cedecea, Cupriavidus, and Ralstonia maintained high relative abundances under the anaerobic recharge. Our study provides essential information about the characteristics of bacterial-mediated hydrochemical reactions during the MAR process. The result would enhance understanding of MAR activities and provide valuable insights into the groundwater resources’ sustainable development and management.