The Brabrand Sø area west of Aarhus in eastern Jylland, Denmark, was deglaciated about 18 000 to 17 000 years ago. Coring in the present-day lake area revealed Early Holocene stream deposits overlain by marine deposits. The area was transgressed by the sea at c. 8500 cal. years BP and a 12 km long, narrow fjord was formed. In the beginning, the fjord housed a species-poor marine or brackish-water fauna with molluscs Hydrobia sp. (mudsnail), Littorina littorea (winkle), Mytilus edulis (blue mussel) and Cerastoderma sp. (cockle). This phase was followed by a phase during which the fjord housed a species-rich fauna that included Ostrea edulis (European flat oyster) and Ruditapes decussatus (palourde clam). During this phase the salinity and summer water temperatures were higher than in present day Aarhus Bugt and we also see evidence for strong bottom currents. This phase was probably characterised by a fairly large tidal amplitude. Two radiocarbon ages of O. edulis shells of c. 6250 and 6700 cal. years BP indicate that such conditions peaked during the period of the Ertebølle culture. The high-salinity phase was followed by a phase with a more species-poor fauna, this phase was also characterised by a high sedimentation rate – a feature seen in other fjords in the region. We suggest that the shift could be due to a decrease in tidal amplitude. Brabrand Fjord was eventually transformed into a lake due to land uplift and closure of the connection to Aarhus Bugt due to longshore sediment transport but the timing of the transition from fjord to lake is still unknown.