Nutrient enrichment of aquatic bodies increases N and P concentrations and may affect the trophic interactions of communities. Benthic microalgae assemblages are regulated by both abiotic (e.g., nutrient) and biotic (e.g., grazing) factors. Here, we focus on how benthic communities have changed along the seasonality and availability of nutrients in reservoir waters. We used three reservoirs from the Neotropical semi-arid region to investigate changes in water nutrient concentrations that determine the structural attributes of microalgae and how food quality (algae group dominance) is reflected in the density and taxonomic richness of herbivorous macroinvertebrates. These environments sustain a benthic macroinvertebrate community dominated by scrapers, while at the same time, we found a community of microalgae represented mainly by cyanobacteria and diatoms at different concentrations of nutrients. Changes in macroinvertebrate structure were evidenced mainly by the availability of cyanobacteria and diatoms. During the rainy season, herbivorous macroinvertebrates densities showed an inversely proportional relation to high cyanobacteria densities. Cyanobacteria have morphology, toxin production, and mucosaccharide sheaths that make them impalpable to herbivores by reducing the population density of consumers. During the dry period, the density of herbivorous macroinvertebrates increased, coinciding with diatom dominance. Diatoms are used as food sources for many consumers because they arc rich in protein and fatty acids. In the eutrophic environments studied, the changes in the trophic relationships of the communities were evident according to nutrient concentrations during the seasons. The grazing effect of herbivores on microalgae was insufficient to cause any significant reduction, while high levels of nutrients caused bottom-up changes in the highest levels of the food web, demonstrating that this complex interaction is influenced by several factors.