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Habitat complexity is recognized to mediate predator–prey relationships by offering refuge or not. We investigated the availability of planktonic microcrustaceans and the diet of a planktivorous fish (Hyphessobrycon eques) at different levels (low, intermediate and high) of aquatic macrophyte biomass. Sampling was carried out in a river with low flow speed, located in a Neotropical floodplain. We collected fish and microcrustaceans in macrophyte stands with variations in biomass. There were no differences in microcrustacean density in the water among the levels of macrophyte biomass, but microcrustacean richness and diet composition of H. eques differed. Microcrustacean richness and trophic niche breadth of the planktivorous fish were higher in high biomass stands. There was high consumption of a small cladoceran species in low macrophyte biomass, which was replaced by larger species, such as copepods, in intermediate and high biomass. Thus, the selection of some species was different among the biomass levels. These results suggest that plant biomass plays an important role in the interaction between fish and microcrustaceans, and prey characteristics such as size, escape ability and energy value make them more or less subject to predation by fish according to habitat structuring.