A network of 26.570 water-body catchments in Germany was derived from the hydrologically-defined drainage basins of the German federal states. To these drainage basins, we assigned the longest intersecting or the next downstream water-body code. Spurious intersections were removed. As the official water bodies may be ecologically but not hydrologically well defined, we split them at confluences and intersections to create extended water bodies. The final WB network contains 11.005 out of the 11.586 original water bodies longer than 1 m. The assigned catchment areas range from <<0.0001 to 446 km², with a median of 10 km². The dataset combines the requirements of hydrological and ecological modelling applications at basin or national scales with the needs of the EU reporting.