Changes in the functional groups of zooplankton were studied in autumn in a temperate floodplain lake (Lake Sakadaš, Kopački Rit Nature Park, Croatia) and in the Drava River (in the Croatian part of the river). Various abiotic parameters as well as available food sources (phytoplankton and microphytes (algae and cyanobacteria) developing on epixylon, epilithon and artificially introduced microplastics called “plastisphere”) were also studied. The lake was hydrologically isolated from the main river during the study, while the water level of the Drava River fluctuated, resulting in larger variations in limnological parameters. Due to stable conditions in the lake, zooplankton abundance, biomass, and species richness were higher than in the Drava River. In both environments, zooplankton species feeding on bacteria, detrital suspensions, and small algae were most abundant, with predators and microfilter-feeders being more abundant in the lake. Microphytes were diverse and mostly small and medium-sized in phytoplankton and all substrate types. Stable lake conditions promoted higher abundance of the zooplankton group, which effectively uses larger algae as a food source. The lower abundance of zooplankton feeding on larger algae and predatory species in the river suggests that the epilithon and plastisphere community was a less mature community compared to the lake, and the heterotrophic component with ciliates and/or other small heterotrophs was not well developed. The importance of plastispheres was particularly evident under the turbid hydrologic conditions that prevailed in the river at the end of the study, when phytoplankton biomass decreased and zooplankton abundance steadily increased, suggesting that microphytes colonised on microplastics were an additional food source for higher trophic levels.