Trophic interaction in tropical regions is influenced by factors such as the size of organisms and the presence of intermediate predators. Macrophytes can act directly on predator–prey dynamics through the habitat structure provided by plants. We conducted an in situ mesocosm experiment (100 L) in a Brazilian reservoir to evaluate the top-down and bottom-up control promoted by the fish Astyanax lacustris, and to evaluate the effects of floating and submerged macrophytes’ morphology on trophic interaction. The experiment lasted ten days and consisted of four treatments in triplicate (n = 12): a control (C) without fish, with only the natural plankton community, and treatments with addition of fish (+ F), fish + floating macrophyte (+ FFM) and fish + submerged macrophyte (+ FSM). In treatments with macrophytes, artificial plants were added to serve as shelter for zooplankton and Chaoborus. Our results showed that fish reduced small cladoceran and Chaoborus biomass by top-down control and increased edible phytoplankton biomass by increasing nutrient concentrations by bottom-up control. Chaoborus increased the food chain length to four levels, with negative effects on the biomass of small cladocerans. Submerged macrophytes were more efficient in providing refuge for copepods and Chaoborus. In general, planktivorous fish had a direct effect on zooplankton and an indirect effect on phytoplankton, and the invertebrate Chaoborus interfered with the functioning of trophic networks. Our results show that, in experimental conditions, macrophytes can play a fundamental role in tropical reservoirs by reducing the strength of top-down control in the trophic cascade.