<p>The widespread use of herbicides has unknown and unexplored consequences for the aquatic ecosystem; herbicides based on the active ingredient flumioxazin have been used effectively for agriculture to control broad-leaved weeds. In this sense, this study investigated the direct effects of the flumioxazin-based herbicide on the microalgae <i>Raphidocelis subcapitata</i> and the impact of stressed algae used as the food source for zooplankton organisms <i>Ceriodaphnia silvestrii</i> and <i>Daphnia magna</i>. The results revealed that the microalgae showed high sensitivity to the herbicide, showing phytotoxicity from 2.726&#xa0;µg L^− 1 with the effective concentration of 50% (EC₅₀) of 4.57&#xa0;µg L^− 1. Carbohydrate accumulation was also observed in response to the presence of flumioxazin-based herbicide. Furthermore, the filtration and ingestion rates of cladocerans in response to microalgae contaminated with the herbicide were found to be altered and specific to each species. The differences in body size and individual dietary needs among the species resulted in variations in the amount of phytoplankton ingested. However, at the EC₅₀ found for microalgae, the ingestion of cladocerans was not altered, suggesting adequate adaptation to the available food. However, a reduction in the filtration rate was observed for <i>D. magna</i>. These results emphasize the importance of considering the different effects of herbicides at different trophic levels of aquatic ecosystems, showing that microcrustacean feeding can be a crucial factor in determining the impact of these chemicals on an ecosystem, since stress suffered by algae at the lower trophic level can propagate to higher trophic levels.</p>