This study enhances the understanding of riverbank filtration and improves management of the Mississippi River valley alluvial (MRVA) aquifer during a managed aquifer recharge (MAR) pilot project at Shellmound, MS. Using high-resolution electrical resistivity tomography (ERT) and self-potential (SP) geophysical methods, we characterized the heterogeneous MRVA aquifer and monitored groundwater flow near a pumping well. ERT was used to provide detailed spatial characterization, filling gaps left by airborne electromagnetic (AEM) data and soil boring logs, while SP techniques were used to monitor groundwater flow, predict drawdown trends, and investigate surface-groundwater interactions. Results showed that SP signals were influenced by groundwater flow, river infiltration, and water mixing due to pumping disturbance of natural geochemical stratification, with significant river interaction observed after 1 h of pumping. The integration of ERT and SP methods revealed lithologic heterogeneity, explaining greater drawdowns on the northern side of the well and increased flow from the riverside. This comprehensive approach offers valuable insights into aquifer management and sustainability.