Variable hydrology of rivers strongly affects biophysical factors that influence primary production and population densities, thereby affecting the relative influence of bottom-up and top-down processes in trophic networks. Many tropical floodplain rivers have sustained seasonal flood pulses driven by precipitation patterns of the Intertropical Convergence Zone. These changes in flow alter concentrations of dissolved nutrients, aquatic primary productivity, and per-unit-area densities of aquatic organisms. Therefore, one would predict that the strength of top-down effects of animals on basal resources should shift as the annual flood pulse progresses. We conducted a series of field experiments in a Neotropical lowland river to test for effects of hydrologic phase, habitat (in-channel vs. floodplain aquatic habitat), and benthic feeding fish and meiofauna on particulate organic matter, chlorophyll, and benthic microalgae. Net ecosystem productivity of this oligotrophic river is higher during the low phase of the annual flood cycle, which is also when resident fishes are at highest densities and there is a seasonal influx of migratory benthic feeding fish. We therefore hypothesized that top-down effects of benthic-feeding fish would fluctuate temporally, with strongest effects during low water levels. We found that fish controlled the abundance of particulate organic matter and algae on solid substrates, but not on sand, during falling- and low-water phases within both channel and floodplain habitats. Except for diatom assemblages, which responded to fish exclusion, the taxonomic structure of algal and meiofauna assemblages was not significantly influenced by fish exclusion treatments, but varied in relation to habitat type and hydrologic phase. Meiofauna densities were highest during the low-water period; experimental exclusion of meiofauna during this period had a significant effect on accumulation of particulate organic matter in sand. By controlling abundance of important basal resources, fishes and meiofauna have large potential to influence other components of this tropical ecosystem. Our findings emphasize the predictable, gradual, changes in consumer-resource interactions associated with the seasonal flood pulse in tropical river systems.