Marine litter loads in sea compartments are an emergent issue due to their ecological and biological consequences. This study addresses microplastic quantification and morphological description to test spatial differences along an anthropogenic gradient of coastal shallow sediments and further on to evaluate the preferential deposition of microplastics in a given sediment grain fraction. Sediments from Marine Protected Areas (MPAs) contained the highest concentrations of microplastics (MPs): up to 0.90 ± 0.10 MPs/g suggesting the transfer of microplastics from source areas to endpoint areas. In addition, a high proportion of microplastic filaments were found close to populated areas whereas fragment type microplastics were more common in MPAs. There was no clear trend between sediment grain size and microplastic deposition in sediments, although microplastics were always present in two grain size fractions: 2 mm > x > 1 mm and 1 mm > x 0.5 mm. •MPs loads are greater in marine protected areas than in the urbanized coastal zone.•Filaments are found in areas close to urbanization.•MPs are present in all sediment grain sizes of 2 mm > × > 1 mm and 1 mm > × 0.5 mm.•There is spatial variability in MP deposition in shallow coastal sediments.