Late- and postglacial geological evolution of the southern Kattegat connection to the Great Belt was investigated from high-resolution seismic data and radiocarbon-dated sediment cores in order to elucidate the Ancylus Lake drainage/Littorina Sea transgression. It was found that glacial deposits form the acoustic basement and are covered by Lateglacial (LG) marine sediments and postglacial (PG; Holocene) material. The LG deposits form a highstand systems tract, whereas the PG deposits cover a full depositional sequence, consisting of a lowstand systems tract (PG I), transgressive systems tract (PG II; subdivided into three parasequences) and finally a highstand systems tract (PG III). PG I sand deposits (11.7–10.8 cal. ka BP) are found in a major western channel and in a secondary eastern channel. PG II (10.8–9.8 cal. ka BP) consists of estuarine and coastal deposits linked to an estuary located at the mouth of the channels. Both channels drained fresh water from south to north. The PG III, that is younger than 9.8 cal. ka BP, represents the threshold marine flooding at the southeastern branch of the palaeo-Great Belt channel. At 9.3 cal. ka BP, fully marine conditions were established, shortly before the flooding of the threshold to the northern part of the Great Belt. These early Holocene spits and sand bars are preserved as features on the present seabed, probably as a result of the rapid sea-level rise that led to back-stepping of the early Holocene palaeo-coast system. This study shows no evidence of major erosion or delta deposition linked to the emptying of the Ancylus Lake, which suggests that continuous water flow from the south characterized the area, without any major drainage event of the Ancylus Lake impacting the southwestern Kattegat.