Exploration of the underwater landscape in Lithuanian waters, in the eastern part of the Baltic Sea, allowed identification of trees stumps in growth position, peat sediments, and traces of people that were living in the now flooded landscape. The exploration has been concentrated on localisation of the former Early Holocene coasts. Based on new data about sediment layers of the Preboreal‒Atlantis I, palynological and dendrohronological analysis, identified vegetation species, and dating of wood and peat samples by radiocarbon methods the Baltic Sea water level dynamics during the stages Yoldia Sea‒Early Litorina Sea could be identified. There are traces of the eroded coasts of the Yoldia Sea at a depth of 39–43 m, which were also observed at depths of 44 and 47 m. During the Ancylus Lake transgression, the RF‐I lagoons and small lakes with the peat layer and the surrounding forests were submerged. The water level could have even risen to 10–9 m below present sea level. The water drop during the Ancylus Lake regression is evidenced by a peat layer dated to 9,150–8,520 cal BP, and similar radiocarbon dating of an oak stump. The changes of the species composition of trees are indicative of the noticeable climate changes during the period 11,410–7,900 cal BP. Litorina transgression is marked by a tree stump found at a depth of 14.5 m dated to 7,900–7,660 cal BP. The preference of the Early Holocene population to the coastal zone is evidenced by poles driven into the seabed (one was dated to 9,510–9,460 cal BP) that were detected at a depth of 11 m and the T‐shaped antler axes dated to the Early Neolithic, washed ashore from the Litorina Sea coastal Stone Age settlements.