Although riverbank filtration (RBF) has been widely applied in China, the managers do not pay enough attention to the inevitable clogging issues during continuous RBF operation. The RBF site, which is located near the Lalin River, northeastern China, was selected as the study area, and the laboratory column experiments were used to simulate the RBF process and further investigate the physical and chemical clogging. The removal of turbidity (59.4–95.1%), COD (21.9–71.7%), NH4+ (10.9–39.4%), Fe (18.5–64.8%), and Mn (19.8–71.7%) demonstrated the water quality improvement by RBF. Whereas, the significant decrease in permeability (39.6–88.2%) also indicated that the clogging issues could not be ignored during RBF. Among them, the physical clogging-dominated area, chemical clogging-dominated area, and the transition zone were located at 0–12.5%, 37.5–100%, and 12.5–37.5% of the infiltration pathway, respectively. Moreover, the concentration of suspended particle materials, mean size of riverbed sediments, and aquifer media are the major impact factors for physical clogging; the precipitation of soluble constituents and redox reaction and other hydrochemical processes were the major impact factors for chemical clogging. The conclusion of this study can contribute to managers alleviating the clogging issues and improving the effectiveness of the sustainable operation in the local RBF system.