Groundwater serving as a drinking water resource usually contains manganese ions (Mn²⁺) that exceed drinking standards. Based on the Mn biogeochemical cycle at the hydrosphere scale, bioprocesses consisting of aeration, biofiltration, and disinfection are well known as a cost-effective and environmentally friendly ecotechnology for removing Mn²⁺. The design of aeration and biofiltration units, which are critical components, is significantly influenced by coexisting iron and ammonia in groundwater; however, there is no unified standard for optimizing bioprocess operation. In addition to the groundwater purification, it was also found that manganese-oxidizing bacteria (MnOB)-derived biogenic Mn oxides (bioMnO_x), a by-product, have a low crystallinity and a relatively high specific surface area; the MnOB supplied with Mn²⁺ can be developed for contaminated water remediation. As a result, according to previous studies, this paper summarized and provided operational suggestions for the removal of Mn²⁺ from groundwater. This review also anticipated challenges and future concerns, as well as opportunities for bioMnO_x applications. These could improve our understanding of the MnOB group and its practical applications.