The zooplankton research was conducted during the summer period of 2012 in three water bodies of different origins, morphometry, trophic level, coverage and composition of macrophytes: on the back water of the Sutla River, oxbow Škrčev kut and gravel pit Zajarki. The main hypotheses of this study were: (i) width of macrophytes stands and their architecture significantly impact diversity and abundance of zooplankton as well as fish predation; (ii) macrophyte stands affect the abiotic and biotic factors of aquatic ecosystems. The research goals were to determine: 1) diversity and abundance of zooplankton in lakes with submerged and floating macrophyte stands; 2) impact of fish predation on composition and size structure of zooplankton in lakes with different stands of macrophytes; 3) impact of macrophyte and fish predation on zooplankton fecundity. The analysis of physico-chemical parameters showed statistically significant spatial differences between three water bodies which affected the composition of the biocenoses and macrophytes coverage. The highest abundance of zooplankton and females with eggs was recorded in eutrophic oxbow Škrčev kut, with medium coverability of floating macrophytes, while the lowest abundance and diversity of zooplankton was observed in the gravel pit Zajarki with high transparency and low trophic level. The back water of Sutla River is separated in the Upper basin with higher transparency and macrophyte coverage, higher zooplankton diversity and more pronounced fish predation, and in the Lower basin of higher turbidity, without macrophytes, smaller diversity where detritivorous species of Rotifera and Copepoda accomplished higher abundance. Stations that have recorded the higher abundance and diversity of zooplankton were in the littoral zone, which confirmed the role of macrophytes as a shelter from predation pressure. Fish predation affected on zooplankton and females with eggs horizontal migration in the littoral zone with macrophytes or their vertical migration into the deeper water layers. At all three locations in zooplankton composition dominated Rotifera with Kerratella cohlearis, Trichocerca similis and Brachionus species, Copepoda with Macrocyclops albidus and larval stages while in Cladocera dominated species was Bosmina longirostris.