Along parts of the Hanö Bay coast in south-eastern Sweden, remains of a submerged landscape can be found down to depths of almost 25 m b.s.l. The coastal landscape was formed during two periods of lowered water levels in the Baltic Basin: the Yoldia Sea and the Initial Littorina Sea stages. In order to reconstruct the local environment and shoreline displacement during the Yoldia Sea and Ancylus Lake stages, sediment sequences were obtained at 4.5, 17.5 and 18.7 m b.s.l. Detailed bathymetric mapping was based on multi-beam echo-sounding while surveillance and sampling of tree remains and archaeological findings were performed through diving. The Yoldia Sea low-stand reached its minimum level at 24–25 m b.s.l. just before 10,800 cal. BP. During the subsequent Ancylus transgression, a slow-flowing river passed through the area, accumulating thick deposits of fine-grained organic sediments in lagoonal basins. The river was surrounded by open woodland dominated by pine. Based on successive flooding of rooted tree stumps, the transgression rate was estimated at 4 cm·yr−1, until the Ancylus high-stand was reached at 5 m b.s.l. at 10,400–10,300 cal. BP. Findings of worked aurochs and beaver bones provide evidence of human presence in the landscape and show the importance of terrestrial resources for their subsistence. These integrated palaeoecological and archaeological investigations demonstrate the importance of submerged landscapes with well-preserved sediment, wood and bone material for our understanding of southern Baltic coastal landscapes and their inhabitants during the Early Mesolithic.