A high-resolution study of palaeoenvironmental changes through the late Younger Dryas and early Holocene in the Skagerrak, the eastern North Atlantic, is based on multiproxy analyses of core MD99-2286 combined with palaeowater depth modelling for the area. The late Younger Dryas was characterized by a cold ice-distal benthic foraminiferal fauna. After the transition to the Preboreal (c. 11 650 cal. a BP) this fauna was replaced by a Cassidulina neoteretis-dominated fauna, indicating the influence of chilled Atlantic Water at the sea floor. Persisting relatively cold bottom-water conditions until c. 10 300 cal. a BP are presumably a result of an outflow of glacial meltwater from the Baltic area across south-central Sweden, which led to a strong stratification of the water column at MD99-2286, as also indicated by C. neoteretis. A short-term peak in the C/N ratio at c. 10 200 cal. a BP is suggested to indicate input of terrestrial material, which may represent the drainage of an ice-dammed lake in southern Norway, the Glomma event. After the last drainage route across south-central Sweden closed, c. 10 300 cal. a BP, the meltwater influence diminished, and the Skagerrak resembled a fjord with a stable inflow of waters from the North Atlantic through the Norwegian Trench and a gradual increase in boreal species. Full interglacial conditions were established at the sea floor from c. 9250 cal. a BP. Subsequent warm stable conditions were interrupted by a short-term cooling around 8300-8200 cal. a BP, representing the 8.2 ka event.