Eutrophication is a process characterized by the enrichment of a given aquatic environment with nutrients, triggering a serious and growing ecological problem in continental aquatic ecosystems, including effects on the biodiversity and ecosystem functioning. For this, we predicted that eutrophication decreases zooplankton functional richness, evenness, divergence and dispersion, and changes the functional composition of zooplankton. Zooplankton and water features were sampled in sixteen shallow ponds in northeastern Brazil. Functional diversity aspects were calculated for each assembly (rotifers, cladocerans, and copepods) using multidimensional indexes and functional groups. Principal component analysis, multiple linear regression, hierarchical cluster analysis and distance-based redundancy analysis were performed to characterize the environmental variation, and to identify associations with functional zooplankton diversity. We observed that turbidity and increased nutrients influenced the functional composition and functional diversity indices of zooplankton due to aquatic pollution. Eutrophic environments favored more specialized species, with greater selectivity in food capture and greater ability to escape predators. We suggest that eutrophic conditions lead to changes in the functional composition of the assemblies decreasing differentiation and variability of functional traits. Such changes lead to a loss of ecosystem processes and make these ecosystems more vulnerable.