Saltwater intrusion (SWI) is a critical concern affecting coastal groundwater sources due to natural and anthropogenic activities. The health of coastal aquifers is deteriorated by excessive SWI, mainly caused by the disturbance of the freshwater–saltwater equilibrium due to the escalating population, climate change, and the rising demand for freshwater resources for human activities. Therefore, gaining insight into the dynamics of SWI is crucial, particularly concerning the various factors that influence the intrusion mechanism. The present study focuses on the experimental simulation of saltwater in freshwater aquifers, considering boundary conditions and density-dependent effects. Two geological scenarios within coastal environments were investigated: First, a uniform, homogeneous case consisting of only sand, and second, a heterogeneous case in which layers of sand, clay, and sand mixed with pebbles are used. During the experiment, DC resistivity sounding data, as part of a widely recognized geophysical method, were collected and subsequently inverted to determine the depth of the freshwater–saltwater interface (FSWI). A finite element analysis was employed to generate numerical models based on experimental feedback. Further, for validation purposes, electrical resistivity tomography (ERT) data were collected from two distinct locations: near the seacoast and an aquaculture area. The ERT results show the presence of salinity intrusion in the study area, attributed mainly to groundwater overpumping and fish farming practices. The experimental findings indicate that the advancement of saltwater is affected by the geological properties of the media they traverse. The porosity (ϕ) and permeability (k) of the geological layer play a crucial role during the passage of saltwater flux into freshwater aquifers. The FSWI deviated along the clay boundary and hindered the easy passage of saltwater into surrounding layers. The alignment of experimental, numerical, and geophysical data suggests that this integrated approach could be valuable for studying SWI and can be applied in different geological settings, including tidal flats and alluvial plains.