We present a high-resolution paleogeographic reconstruction of the Baltic Sea for the Holocene period by combining eustatic sea-level change, glacio-isostatic movement, and sediment dynamics. In the northeastern part, morphological change is dominated by regression caused by post-glacial rebound that outpaces the eustatic sea level rise, whereas a transgression, together with active sediment erosion/deposition, constantly shapes the coastal morphology in the southeastern part.