We assessed the zooplankton assemblages in four temperate shallow waterbodies differing in macrophyte coverage and alternative states: transparent vs. turbid. The main objectives of this study were: (i) to determine the horizontal assemblage of zooplankton in structurally different habitats; (ii) to examine the role of fish, macroinvertebrates and environmental conditions in the observed zooplankton assemblage patterns; and (iii) to evaluate the zooplankton-macroinvertebrate-fish food web interactions in pelagial and littoral zone in transparent vs. turbid lakes. Abiotic factors and food resources, as well as zooplankton assemblage did not show significant difference along the gradient of habitat complexity, but exhibited pronounced variability among these waterbodies. Selected lakes contained nutrient levels that can undergo or were shifted into turbid state. Two waterbodies showed hysteresis: at similar nutrient conditions one remained transparent with macrophytes, while other shifted in its turbid state with increased phytoplankton biomass, and reduced population of planktonic crustaceans. Rotifers contributed mainly to the metazooplankton diversity and abundance. The results suggested that total phosphorous and phytoplankton were the main drivers in turbid waterbodies, and biotic interactions governed structuring of zooplankton assemblage in transparent waterbodies. Habitats of submerged and floating-leaved macrophytes do not appear to a secure refuge for zooplankton against predation. On the other hand, sediment in the vegetated and non-vegetated littoral zone functioned as an effective shelter. According to our results, zooplankton underwent strong predation pressure by macroinvertebrates and small-sized fish in the littoral and by larger-sized fish in pelagial, with alteration related to ecosystem peculiarities. Based on an applied ecological network model, zooplankters were equally vulnerable to predation in both the pelagial and littoral zones, and these biotic interactions were main factors for zooplankton homogenous horizontal distribution. These results suggest that zooplankton organisms play important role in the matter cycling and resilience of the food webs to environmental alterations.