Although anthropogenic activities are widely recognized as a major threat to marine biodiversity, their impacts have not been fully assessed and there is an urge to improve the understanding of the magnitude and mechanisms of those impacts. In this study, we used DNA metabarcoding-based methods to investigate plankton biodiversity patterns under varying anthropogenic pressures (i.e., shipping and bivalve aquaculture) along the eastern Adriatic coast. Our study determined similar community structures among investigated coastal locations in three geographic regions in the Adriatic Sea, as well as between shipping ports and aquaculture sites.