In coastal waters the identification of sources, trajectories and deposition sites of marine litter is often hampered by the complex oceanography of shallow shelf seas. We conducted a multi-annual survey on litter at the sea surface and on the seafloor in the south-eastern North Sea. Bottom trawling was identified as a major source of marine litter. Oceanographic modelling revealed that the distribution of floating litter in the North Sea is largely determined by the site of origin of floating objects whereas the trajectories are strongly influenced by wind drag. Methods adopted from species distribution modelling indicated that resuspension of benthic litter and near-bottom transport processes strongly influence the distribution of litter on the seafloor. Major sink regions for floating marine litter were identified at the west coast of Denmark and in the Skagerrak. Our results may support the development of strategies to reduce the pollution of the North Sea.