The ‘Wadden Sea Archive of landscape evolution, climate change and settlement history’ project (WASA) focuses on the analysis of marine sediment archives from the East Frisian Wadden Sea region. It aims at understanding the formation of palaeolandscapes since the end of the last ice age. One part of the project studies the possible correlation and shift of archaeological settlement patterns, climate change and sea-level rise through time in order to derive archaeological expectancy maps. In this paper we present our findings for a quantifiable set of Stone Age sites in the area of the prehistorical Dornumer tidal basin, discussing them against the background of coastal environmental factors and the applied methodology of our modelling. To enable spatial analysis of these sites, we developed a palaeographic elevation model, which was subsequently flooded at 2000-year intervals between the Boreal and early Subboreal periods. Particular challenges are posed by the dynamics of marine transgression, the related changes in the natural environment and their spatial extent. As a result of our GIS-based approach, the model can be extended geographically and provides a basis for future research.