Saltwater intrusion (SWI) in coastal aquifers poses a significant threat to freshwater resources, exacerbated by climate change and rising sea levels. This study investigates SWI dynamics using laboratory experiments, geophysical monitoring with the self-potential (SP) method, and numerical simulations to assess the impact of varying salt concentrations (7 g/L and 35 g/L) on intrusion rates and electrochemical responses. Laboratory experiments were conducted in a custom-designed sandbox model, with SP data collected in real time using a 192-electrode system. Numerical simulations were performed to replicate experimental conditions and validate the model’s predictions. Results show that salt concentration significantly influences intrusion rates and SP responses. In low-salinity systems (7 g/L), SP values increased gradually from 0 mV to 20 mV, with a slow intrusion rate of 0.034 m/h. In contrast, moderate-salinity systems (35 g/L) exhibited rapid SP changes (0 mV to 5 mV) and a faster intrusion rate of 0.1 m/h. Sharp SP anomalies near the intrusion source, with values dropping from 10 mV to −40 mV, were observed in low-salinity systems, highlighting localized charge imbalances. The model’s performance was evaluated using relative RMSE, showing a good fit in Experiment (1) (RMSE = 5.00%) and acceptable results for Experiment (2) (RMSE = 23.45%). These findings demonstrate the potential of the SP method for real-time monitoring of SWI and provide insights for improving management strategies in coastal aquifers.