The macrozooplankton and littoral macrozoobenthos community were investigated in the Prošće and Kozjak Lakes of the Plitvice Lakes National Park. Macrozoobenthos samples in the littoral zone were collected by hand net up to 1 m depth at five stations in both lakes, and macrozooplankton samples at every 5 m depth from the water surface to the deepest point of the lake. In addition to sample collection, physicochemical water parameters were also measured. Macrozoobenthos was sampled in the summer of 2018, and macrozooplankton in the vegetation period of 2009. The aim of the study was to compare the composition and structure of macrozoobenthos and macrozooplankton communities between the two largest lakes in the Plitvice Lakes National Park, the interactions of communities with respect to the degree of trophy, and the potential of macrozoobenthos in indicating hydromorphological changes. The diversity of macrozoobenthos is greater in Kozjak Lake in comparison with Prošće Lake. Greater coverage of macrophytes does not necessarily lead to greater abundance and diversity of macrozoobenthos. Kozjak Lake has a higher abundance and biomass of macrozooplankton compared to Prošće Lake. The diversity and trophic structure of macrozooplankton can be indicative of the trophy level of the lake.