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Riverbank filtration (RBF) is an important part of the surface water–groundwater cycle, and it intercepts and retains many pollutants in rivers. However, RBF affects the biogeochemical process which enables aquifer sediments to release iron (Fe) and manganese (Mn). In this study, column experiments were performed to investigate the effects of ammonium ions and organic matter on Fe and Mn release from anaerobic RBF sediments. In addition, high-throughput sequencing technology was used to characterize the microbial community. The results showed that the ammonium ions (NH₄⁺) and organic matter (COD) in groundwater promote the release of Fe and Mn from aquifer sediments. The trends of Fe and Mn release were similar during the leaching process. The maximum concentrations of Fe and Mn were 0.32 and 40 μg/L, respectively. The structural diversity and abundance of the microbial communities in the groundwater were closely related to the Fe/Mn content. <i>Actinobacteriota</i>, <i>Proteobacteria</i>, <i>Acidobacteriota</i>, <i>Bacteroidota</i>, and <i>Chloroflexi</i> were the dominant phyla, while <i>Rhodococcus</i>, <i>Ochrobactrum</i>, and <i>Pseudarthrobacter</i> were the dominant genera. These functional microbes are actively involved in the biogeochemical cycling of Fe, Mn, and N. In summary, contaminants and the microbial-community structure have dual effects on the release of Fe and Mn from RBF aquifers.