Abstract. Abstract: Aim Zooplankton functional groups play an important role in lake functioning and can readily respond to environmental changes and may be associated with phytoplankton changes. In warmer regions, zooplankton species have a smaller body size, which decreases their grazing capacity, attenuating top-down control throughout phytoplankton. We evaluated changes in density and biomass of zooplankton functional groups and their relationship with algal groups in horizontal reservoir zonation (pelagic, sublittoral, and eulittoral zones) of the shallow reservoir. We hypothesize that the density and biomass of zooplankton functional groups are associated with fluctuations in the phytoplankton groups in horizontal reservoir zonation. Methods Changes in the structure of the zooplankton functional group and the controlling limnological variables were verified at three sampling stations: pelagic, sublittoral, and eulittoral zones in a mesotrophic reservoir. Results Zooplankton species were distributed in seven functional groups. The density and biomass of zooplankton functional groups were not clearly associated with biomass variations of phytoplankton groups. However, the zooplankton functional groups were associated with horizontal reservoir zonation, where specific groups were found in the pelagic, sublittoral, and eulittoral zones. Conclusions The zooplankton functional groups were related to the horizontal zonation of the reservoir but were not associated with changes in the phytoplankton groups due to the dominance of small organisms.