The effect of tides and waves complicates groundwater flow dynamics in subterranean estuaries. Geological variations in coastal aquifers increase complexity and may affect flow dynamics differently than in homogeneous settings. Thus, intruding seawater might change how nutrients, contaminants, and metal fluxes of the terrestrial groundwater are transported through the intertidal mixing zones, how long these elements stay within the zones, and what biogeochemical reactions can occur. Despite coastal aquifers being heavily influenced by natural geological heterogeneities, most previous submarine groundwater discharge (SGD) studies assumed homogeneous sediment conditions in both numerical and physical models. Moreover, most of the SGD studies accounting for aquifer heterogeneity are numerical studies. Additionally, detecting, tracking, and recording such intricate flow dynamics in the field are challenging. Examining the flow instabilities in artificial coastal aquifers with spatially distributed hydraulic conductivities allowed us to visually assess the coastal flow dynamics, thereby addressing this knowledge gap. We improved our physical sand tank configuration depending on previous successful laboratory experiments and incorporated aquifer heterogeneities—i) as a layer cake and ii) as a brick-like structure in this study. Our results imply that flow instabilities exist in heterogeneous configurations even if the size of the upper saline plume (USP) may shrink due to the presence of low hydraulic conductivity layers; especially for a gentle beach slope (1:12). However, lower hydraulic conductivity layers or compartments may hinder salt fingers from vertical penetration. Furthermore, it is evident that three-dimensionality plays a significant role even in narrow sand tanks. Although the scaling in physical models is different from that of real aquifers, the present work will help to assess the effect of heterogeneity on groundwater flow and transport in coastal aquifers. Furthermore, it will be useful in enhancing long-term water management strategies for coastal aquifers in the wake of climate change.