The river infiltration zone is a mixed area of surface water and groundwater under the riverbed and along the riverbank, which is greatly affected by river infiltration. Currently, there is a lack of understanding regarding the migration and transformation processes of Fe, Mn, and As, along with their correlation with organic carbon in the river infiltration zone affected by riverbed scouring and siltation processes. In this study, based on techniques such as pore water sampling and the Tessier sequential extraction, the spatiotemporal variations in Fe, Mn, and As concentrations and possible geochemical processes at the riverbed sediment–water interface and along the river infiltration flow path were revealed. The results indicated that the potential geochemical activity of Fe, Mn, and As and the distribution of organic carbon in the riverbed sediment responded to riverbed scouring–siltation processes. Compared to the high water level period, the potential geochemical activity of Fe, Mn, As, and organic carbon in the riverbed sediment generally exhibited an upward trend during the low water level period, indicating more intense Fe and Mn biogeochemical reactions. During river infiltration, the labile organic carbon (LOC) was preferentially utilized, and with increasing depth, the sedimentary organic carbon (SOC) continuously transformed into LOC and dissolved organic carbon (DOC). Affected by riverbed scouring processes, the transition time from oxidizing to reducing conditions in the pore water increased, and the Fe, Mn, and As reduction zones moved deeper and farther from the riverbank, resulting in a significant expansion of the groundwater pollution area. The reductive dissolution of iron and manganese oxides/hydroxides and the oxidation of organic matter–bound Fe, Mn, and As were the main biogeochemical processes contributing to the release of Fe, Mn, and As in the river infiltration zone. These research results have crucial theoretical significance and practical application value for the sustainable utilization of groundwater resources and the remediation of groundwater pollution.