This work used experimental and numerical methods to investigate seawater intrusion (SWI) in a complex heterogeneous laboratory-scale aquifer. We started the analysis with a homogeneous isotropic aquifer as a reference case, then moved to heterogeneous layered aquifers. The study also investigated block-wise synthetic aquifers with different configurations. The seawater wedge toe length generally decreased under heterogeneous conditions, while the freshwater–saltwater dispersion/mixing zone generally increased when compared to the homogenous case. The saltwater–freshwater interface shows a distinct gradient change across boundaries at differing hydraulic conductivities. This was attributed to streamline refraction, which caused a reduction to the angle of intrusion when transitioning from high to low permeability zones and vice versa. The refraction also affected the mixing zone, where additional spreading was also observed when transitioning from high to low permeability zones and vice versa. When low permeability zones predominated the shoreline at the saline water boundary, this produced a shorter saline wedge in the horizontal direction, but it was more expanded vertically. This study provides insight into the general processes of SWI in heterogeneous aquifers and could be used as a basis for defining conceptual models of real-world systems. It highlights the capabilities of the image analysis to capture small perturbations.