Marine litter concentration in the Mediterranean Sea is strongly influenced both by anthropogenic pressures and hydrodynamic factors that locally characterise the basin. Within the Plastic Busters MPAs (Marine Protected Areas) Interreg Mediterranean Project, a comprehensive assessment of floating macro- and microlitter in the Pelagos Sanctuary and the Tuscan Archipelago National Park was performed. An innovative multilevel experimental design has been planned ad-hoc according to a litter provisional distribution model, harmonising and implementing the current sampling methodologies. The simultaneous presence of floating macro- and microlitter items and the potential influences of environmental and anthropogenic factors affecting litter distribution have been evaluated to identify hotspot accumulation areas representing a major hazard for marine species. A total of 273 monitoring transects of floating macrolitter and 141 manta trawl samples were collected in the study areas to evaluate the abundance and composition of marine litter. High mean concentrations of floating macrolitter (399 items/km2) and microplastics (259,490 items/km2) have been found in the facing waters of the Gulf of La Spezia and Tuscan Archipelago National Park as well in the Genova canyon and Janua seamount area. Accordingly, strong litter inputs were identified to originate from the mainland and accumulate in coastal waters within 10–15 nautical miles. Harbours and riverine outfalls contribute significantly to plastic pollution representing the main sources of contamination as well as areas with warmer waters and weak oceanographic features that could facilitate its accumulation. The results achieved may indicate a potentially threatening trend of litter accumulation that may pose a serious risk to the Pelagos Sanctuary biodiversity and provide further indications for dealing with plastic pollution in protected areas, facilitating future management recommendations and mitigation actions in these fragile marines and coastal environments.