Well-preserved Late Glacial to Mid Holocene paleolandscapes containing Final Paleolithic to Early Neolithic wetland sites have been found, buried deeply below the Holocene peat and floodplain deposits of the Waasland Scheldt polders during infrastructure works in the harbor of Antwerp, situated in N-W Belgium. During the Middle to Late Holocene, Late Glacial (river) dunes within the floodplain as well as natural levees and point bars along the river flanks were favored locations for Final Mesolithic to Early Neolithic occupation. Available living space was determined by the paleotopography and elevation of the peat, overlaying Late Glacial deposits and rising under the influence of increasing relative sea level. Therefore, an elevation model of the peat base was created using multi-receiver electromagnetic induction survey. Electrical conductivity data of a dune were collected and 1-D inverted, in order to compose a 3-layered soil model with variable electrical conductivity of the top layer (estuarine floodplain deposits) and variable depth to the base of the middle layer (i.e. the peat). The modelled peat base depth was calibrated, validated by depth data from coring and cone penetration measurements and partially replaced wherever depth modelling from inverting the EMI measurements proved inaccurate. Using the resulting peat base elevation model, a paleogeographic map at the time of the modelled end date of nearby Mesolithic-Neolithic transitional Swifterbant culture sites was created by chronologically modelling the peat elevation at that time. The developed paleogeographic mapping methodology is suitable for other periods during the peat development as well. The resulting maps can be used for subsequent archaeological prospection of possible site locations for artefact scatters by core sampling or to contextualize excavated wetland sites.