The research of zooplankton structure was conducted during the vegetated period in pelagic stations on the longitudinal profile of the Sutla backwater, which consists of two interconnected basins. The Upper, with higher transparency and submerged macrophytes and Lower basin, turbid and without macrophyte stands. The objectives of this study were to determine zooplankton structure considering: (i) differences in theabundance, diversity, size structure and functional feeding guilds; (ii) the impact of environmental factors and food resources; (iii) differences in fish predatory pressure ; (iv) the role of bottom water layers as a zooplankton shelter in shallow lakes. The results of statistical analysis of physical-chemical factors revealed significantly higher transparency and the amount of available food reources in the Upper basin, as compared to a higher turbidity and conductivity in the Lowerbasin. In the Upper basin with submerged macrophytes in the littoral zone, abundance and diversity of zooplankton in the pelagial was higher compared to the Lower basin, without macrophytes, with prevailance of detritovorous, microfilter-feeders (Keratella) and algivorous, macrofilter-feeder (Polyartha and Trihocerca) Rotifera. In the Lower basin abundance of planktonic Crustacea was higher compared to the Upper basin, and prevailed microfilter-feeders Cladocera (Bosmina longirostris) and macrofilter-feeders larval and adult stages of copepods (Thermocyclops oithonoides), while the Rotifera were presented with smaller, microfilter-feeders species. Fish predation pressure was more pronounced in the pelagial of Upper basin of highertransparency, indicated by smaller number of Cladocera in the surface layer which wee probably shifted in littoral macrophyte stands. The results of this study indicate the migration of planktonic Crustacea in the vertical bottom layer where their abundance were higher. Although the studied basins were interconnected, results indicate significant differences in the zooplankton structure as a result of the macrophytes impact on changing environmental conditions and fish predation pressure.