The abundance and distribution of microplastics (MP) were evaluated in six “clean” sites (Italian minor islands) and in two “polluted” areas (near the mouth of two major Italian rivers). Samples of MP, plankton and persistent organic pollutants (POPs) were collected using a manta trawl (MA) and a plankton net (WP2), both lined with a 333 µm mesh net. MP have been confirmed to be ubiquitous since they were found at each site, showing an average density of 0.3 ± 0.04 items/m3 (values ranged from 0.641 to 0.119 ). When comparing the clean sites with the polluted ones, a significantly higher value of MP was found near the river mouths. The most common types of MP were synthetic filaments (50.24%), followed by fragments (30.39%), thin plastic films (16.98%) and spheres (2.39%). Infrared spectroscopy analysis highlighted that the most abundant polymers were polyethylene (PE-26%), polypropylene (PP-11%), polyethylene-terephthalate/polyester (PET/PEST-8%) and ethylene-vinyl-acetate (EVA-5%). Polychlorinated biphenyls and organochlorine pesticides were detected in all the samples with a high variability among sites and depths. This study adds to the existing information on the distribution of contaminants across the Mediterranean Sea, and is useful to policy makers who wish to implement effective measures to reduce MP pollution.