A Lagrangian study was conducted in a eutrophic estuary (Guanabara Bay, Brazil) to investigate in situ plankton trophodynamics under the influence of the cold, nutrient-rich South Atlantic Coastal Water in a short-term temporal variability (scale of hours). We tested the hypothesis that the base of the plankton food web is composed of small cells and that microzooplankton is the main consumer of this assemblage. Samples of pico-, nano- and microplankton, as well as copepods, were collected during spring, when the entry of upwelling water in the Bay is commonly observed, and near the surface every 3 h during the 1-day sampling period. Potential predation of dinoflagellates, ciliates, copepod nauplii, copepodites and adult copepods was estimated based on predator-prey size relationships. The main trophic links in the Guanabara Bay food web for the period analysed were nanophytoplankton-copepods, nanophytoplankton-ciliates, and autotrophic dinoflagellates-heterotrophic dinoflagellates. According to microphytoplankton availability, adult copepods could not satisfy their food requirement, and nanophytoplankton represented an important supplementary food source. In fact, diel variations of nano- and microplankton biomass were opposite to that of copepods suggesting predation control by the latter on the former. The trophodynamics of Guanabara Bay, under the influence of upwelling water, resulted in marked differences from other eutrophic estuaries around the world.