During the Late Pleistocene, the Palaeo-Ems system (PES) was one of the major tributary channels feeding the Elbe Palaeovalley (EPV) and formed an important part of the drainage system of the continental northwestern Europe unglaciated hinterland. In this study, a detailed interpretation of high-resolution 2D sub-bottom profiler and Boomer grids were used to map the overall course of the submerged PES channel, as well as its spatial and stratigraphic relationships with other Quaternary geological units in the German North Sea. Mapping of buried tunnel valleys, a lacustrine-fill unit, straight channel structures was also carried out. The sedimentary record of the PES is represented by a low gradient and meandering channel which branched into two major pathways as it approached the EPV western flank. Its upstream to downstream trends, coupled with seaward decreasing gradient and sinuosity, are similar to those visible in present-day river deltas. Both the PES and EPV subsequently formed a combined depositional system, which was successively drowned due to the fast-rising relative sea level that overwhelmed the adaptation capabilities of the joint drainage system. For the first time, this study sheds light onto the PES/EPV morpho-stratigraphic relationships which played a key role in the coastal landscape architecture of the German North Sea since the Late Pleistocene.