The plankton trophic structure of a hypereutrophic tropical estuarine system was evaluated in the dry and wet seasons, as well as during the dry–wet transition period, over 1 year. Correlations between micro- and mesozooplankton abundance and composition and both size-fractioned phytoplankton biomass and abiotic variables were investigated in order to understand seasonal variations in plankton interactions and provide a conceptual trophic model for the plankton community. Rainfall is the main environmental forcing factor for this system, and the plankton community responded accordingly, with different structures during each season sampled. The resulting trophic model shows a multivorous food web, where both longer microbial and shorter herbivore food webs occur simultaneously. Microzooplankton play a crucial role in this ecosystem, linking both small and large phytoplankton to the mesozooplankton. These results have important implications for estuarine management practices, particularly under highly eutrophic conditions.