The Paleo Elbe Valley is the most prominent subsurface structure in the southern North Sea. During the Weichselian (marine isotope stage (MIS) 2), the valley traversed the exposed sea floor and drained the southern margin of the Scandinavian ice sheet. Today the valley is filled with up to 16 m thick sediments, but the responsible processes and drivers remain unknown. To unravel these processes and describe the valley’s evolution with Holocene transgression, we use shallow seismic data and vertical high-resolution grain-size core data. At the base of the western shore, supralittoral fine sands are overlain by a thin layer of clay dated to 9.8 cal. ka BP. The major sediment package consists of marine silt with internal seismic reflectors inclined in a northeastern direction, indicating a sediment transport from the southwest. The valley infill started when the western shore was flooded around 9.6 cal. ka BP and can be divided into two phases. During the first one (9.6–8.1 cal. ka BP) the sedimentation rate was highly driven by wind and waves. The second phase (8.1–5.0 cal. ka BP) was mainly tidal dominated but shows also storm event deposits in the north. Around 5.0 cal. ka BP the valley was almost filled.