The land-lake interface is a unique zone where terrestrial and aquatic ecosystems meet, forming part of the Earth’s most geochemically and biologically active zones. The unique characteristics of this interface are yet to be properly understood due to the inherently high spatiotemporal variability of subsurface properties, which are difficult to capture with the traditional soil sampling methods. Geophysical methods offer non-invasive techniques to capture variabilities in soil properties at a high resolution across various spatiotemporal scales. We combined electromagnetic induction (EMI), electrical resistivity tomography (ERT), and ground penetrating radar (GPR) with data from soil cores and in-situ sensors to investigate hydrostratigraphic heterogeneities across land-lake interfaces along the western basin of Lake Erie. Our Apparent electrical conductivity (ECa) maps matched soil maps from a public database with the hydric soil units delineated as high conductivity zones (ECa > 40 mS/m) and also detected additional soil units that were missed in the traditional soil maps. This implies that electromagnetic induction (EMI) could be relied upon for non-invasive characterization of soils in sampling-restricted sites where only non-invasive measurements are feasible. Results from ERT and GPR are consistent with the surficial geology of the study area and revealed variation in the vertical silty-clay and till sequence down to 3.5 m depth. These results indicate that multiple geophysical methods can be used to extrapolate soil properties and map stratigraphic structures at land-lake interfaces, thereby providing the missing information required to improve the earth system model (ESM) of coastal interfaces.