The wooden structures unearthed in 2012 during archaeological excavation in the courtyard of the Museum of Archaeology and History in Elbląg have been dated using the dendrochronological method to the period between 1245 and 1302, which allows them to be considered to be parts of a Teutonic fortress. The remains of the wooden building located directly on the prehistoric lacustrine sediments created a unique opportunity to reconstruct the near-shore sedimentation of the Drużno Lake. Geological, malacological and palynological methods were applied during the investigation. The results, compared with the ranges of both the Drużno Lake and the Vistula Lagoon, known from previous studies of the region, allowed the correlation of a phase of a deep lake with the “Roman Period”. Rapid shallowing of the lake occurred in the “Migration Period”. The final disappearance of the lake in the area of modern Elbląg occurred in the early Middle Ages.