Zooplankton are widely recognised as being regulated primarily by predators and food availability. In reservoirs, the quantity and quality of food resources are generally affected by the characteristics of the water, which in turn are controlled by the flow pulse generated by operation of the dams. In this study, we investigated the relationship between zooplankton, water quality and food availability (phytoplankton) in eight hydroelectric reservoirs located in Brazil. Samples were collected during the rainy and dry periods between 2008 and 2009. In general, the reservoirs exhibited mesotrophic conditions and Cyanobacteria were the predominant phytoplankton. The results showed that the rotifers Kellicottia bostoniensis, Hexarthra mira, Keratella spp., and Polyarthra vulgaris were present, indicating nutrient-rich environments. In addition, the copepod Thermocyclops decipiens occurred in eutrophic environments. In contrast, the cladoceran Daphnia gessneri and copepod Notodiaptomus henseni were considered indicators of more desirable water quality, owing to their relationship with waters with lower levels of nutrients and suspended solids. The results support the use of these organisms as a useful tool for understanding changes in water quality and in the ecosystem processes involved.