Since the early 1990s, excavations of a protohistoric lakeside settlement in the Korça basin carried out by a French–Albanian archaeological team have induced geomorphological and palynological studies about the sedimentary records of Lake Maliq. These studies allow us to distinguish a series of centennial-scale high and low lake level events between 4200 and 4000 cal BP (2899–2637 BC/2843–2416 BC) and 2600 cal BP (822–671 BC), probably due to large-scale climate changes (in the Mediterranean basin). In addition, the sediment sequence also gives evidence of a millennial-scale trend of lake level rise. It appears to be an interplay between lake level rises and falls against tectonic subsidence of the basin allowing accommodation space for sediment deposition. The variations of the lake's level and the lake's surface area influenced the development and the abandonment of the nearby lakeside settlements (like the tell of Sovjan). In order to prepare an archaeological survey around the now dried up lake, we made a 3D model of the Holocene deposit from the lake including these lake level results, geomorphological mapping, excavation data, numerous core logs, AMS 14 C dating and SRTM DEM data. The GIS model allowed us to propose four palaeogeographical reconstructions of the extension of Lake Maliq: around 14,000 BP, during the Mesolithic (around 9000 BP – 8781–8542 BC), the Early/Middle Bronze Age transition (around 3800 BP – 2310–2042 BC) and the Iron Age (2600 BP – 822–671 BC). A map of the thickness of the sediments above potential archaeological layers is also proposed.