Well fields along rivers withdrawing groundwater through riverbank filtration (RBF) are popular for urban water supply, due to their good performance in assurance for both water quantity and quality. However, RBF sites are susceptible to flood inundation, which has been found to cause increase of N, Fe, and Mn contents in groundwater and threatens water safety, but the geochemical processes have not been fully understood. To bridge this gap, in situ monitoring of hydrodynamics, hydrochemistry, and stable isotopes for river water and groundwater were employed in a RBF site, NE China, to investigate into the geochemical processes in groundwater in RBF sites under long-term inundation. The results indicated that during long-term inundation, recharge from river water increased significantly, and a large amount of O2, NO3− and organic carbon (OC) from oxidizing river water could recharge far-shore groundwater vertically, whereas less NH4+ were input from regional groundwater, leading to a high content of NO3− and low content of the NH4+ in the groundwater. Meanwhile, limited NH4+ would be produced through dissimilatory nitrate reduction to ammonium (DNRA) and mineralization of organic nitrogen (MON). Moreover, along the infiltration path, aerobic respiration and denitrification (DNF) occurred rapidly. CO2 generated from OC oxidization in the two processes enhanced the dissolution of carbonate minerals, which could be used to trace the oxidizing-reducing (O-R) interface between river water and groundwater. As indicated, the inundation can cause the O-R interface which usually distributed near shore to extend to the entire well field during inundation. In this situation, the redox condition of groundwater used to be suitable for SO42− reduction in non-inundation period decreases to the level favoring the reduction of Mn(IV)/Fe(III) oxides during inundation, and the process of Fe2+ precipitation by reacting with HS− is weaken as the inhabitation of SO42− reduction, leading to a significant increase in Fe2+, Mn2+, and As contents, putting well field groundwater at risk of contamination.