Soil characterization in coastal areas is essential for strategic coastal engineering implementation and for understanding the paleo-environmental conditions. However, the severe soil salinization in these regions limited the geophysical measurements to shallow depths and conventional drilling is time-consuming and cumbersome. Here, we integrate remote sensing (RS), direct current resistivity (DCR) and time-domain induced polarization (TDIP) to characterize the soil along the Nile Delta coast. To avoid the impact of the recent humanmade topographic artifacts, a high-resolution digital elevation model is produced using old topographic sheets. Consequently, the defunct Holocene streams/buried channels can be extracted. Regarding multi-temporal multispectral and multispectral RS data, land use–land cover maps (LU–LC) indicate that the sabkha/waterlogged areas significantly increased while coastal sand and sand dunes dwindled with a rapid rate of expansion of new urban areas. Applying linear and nonlinear geophysical inversion schemes, the coastal soil heterogeneities are characterized using 1D/2D resistivity and 2D-TDIP measurements with the consideration of the geomorphologic and borehole data, as well as the cone penetration test (CPTu). The geophysical results indicate that the dominance of sandy sediments occurs along the channels and sand dunes sites. Obviously, the discrimination between saturated coastal sandy and clayey soils cannot be attained using individual 2D-DCR tomograms. On the other hand, clay and silt sediments can be well characterized, where the waterlogged areas are dominant, from the high-resolution TDIP inversion. Accordingly, the present protocol can be readily applied along the deltaic coasts subject to heavy anthropogenic activities for prioritized engineering interventions.