In this paper a novel methodology to assess the risk of marine litter (ML) pollution in the Mediterranean Sea is implemented. In this approach, the hazard component is estimated using a state-of-the-art 3D modeling system, which allows the simulation of floating and sinking ML particles; the exposure component is defined from biodiversity estimates; and the vulnerability is related to ML ingestion rates of each species. The results show that the hot-spots for the ML risk concentrate in the coastal regions, and are mainly conditioned by the biodiversity in the region. A dedicated analysis on the marine protected areas shows that the risk therein is controlled by the proximity to ML sources and that their present-day protection levels are not effective in the case of ML pollution. Only a reduction of ML at the sources could reduce the impact of ML pollution in protected areas.