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Owing to serious influences on well performance, bacteria-induced clogging has become a dilemma for managed aquifer recharge (MAR). During MAR, surface river water is inoculated into aquifer and mixed with groundwater. Therefore, the clogging-functional bacteria may originate from the river water or the groundwater. However, the origin of the clogging-functional bacteria in the aquifer has not yet been well understood. This study conducted a series of laboratory-scale column experiments involving different recharge modes (using river water, groundwater) to simulate the processes of bacteria-induced clogging and used the high-throughput sequencing technology, aiming to elucidate the community characteristics and the origin of the clogging-functional bacteria involved in MAR bioclogging. Analyses of the bacterial-community characteristics showed significant differences between the river water and groundwater. The bacterial-community characteristics of the clogging aquifer in the different recharge modes were similar to each other and have common genera, namely, Acinetobacter , Brevundimonas , Exiguobacterium , Porphyrobacter , Cloacibacterium , and Sphingobium , which suggests that MAR activity could promote bacterial communities to become identical during surface water infiltration into aquifers, despite differences in the bacterial communities present in the subsurface- and surface systems. This knowledge will assist greatly in targeted treatment and prophylaxis of clogging-functional bacteria during managed aquifer recharge. • Clogging occurred in all column experiments involving groundwater and river water. • Bacterial-community features in groundwater were different from those in river water. • Bacterial-community features of biofilms under different recharge modes were similar. • MAR activity might alter the bacterial community to become identical. [ABSTRACT FROM AUTHOR]