The research was conducted in shallow water bodies in Krapina (oxbow) and Sutla (backwater) watershed. The main hypothesis of this study were that littoral zone with abundant macrophytes has a positive influence on zooplankton survival during increased fish predation, where habitats with flotating macrophytes or without aquatic macrophytes in the littoral zone have lower abundance of planktonic crustaceans in comparison to habitats with submerged macrophytes. Main aims of this study were to determine: (i) the influence of fish predation on diversity and abundance of Cladocera and Copepoda in littoral sediment; (ii) fish predation on littoral zooplankton in habitats with different macrophyte abundance and habitats without aquatic macrophytes; (iii) biotic interactions in different habitats of shallow water bodies. The results revealed significantly higher turbidity, phytoplankton biomass, dissolved organic matter and throphic state index in Škrčev kut Oxbow, compared to other study sites. Abundance and diversity of planctonic crustaceans and abundance of crustacean female with eggs were significantly higher in the littoral zone with abundant macrophytes, compared to littoral zone with flotating macrophytes or without macrophytes. With increased turbidity and lower habitat diversity of the littoral zone, fish predation effects and role of the littoral zone as a refuge for zooplankton decreases. The results of this study suggest that presence or abscence of macrophytes can significantly change biotic interactions and biocenosis structure in shallow water bodies, despite similar abundance, diversity and predator body size.