The European Water Framework Directive implements the policies to achieve a good ecological status of all European waterbodies. To determine the ecological potential in freshwater environments, abiotic (morphology, physical and chemical variables) and biotics (algae, fishes, etc.) metrics are used. Despite their importance in trophic web, zooplankton was not included as one of the Biological Quality Elements (BQE) to determine the water quality. In the present research, we studied the zooplankton species that can be considered as indicators of trophic status and ecological potential for more than 60 water reservoirs. The data were obtained from more of 300 samples collected during 10 years from reservoirs at Ebro River watershed, which is the largest basin in Spain. According to their physicochemical and biological elements, the trophic status and ecological potential of these reservoirs were established. More than 150 zooplankton species were identified during the study. The results from this research indicate that species that are related with low water quality are: Acanthocyclops americanus, Ceriodaphnia spp., Daphnia cucullata, Daphnia párvula, Diaphanosoma brachyurum, Brachionus angularis, Keratella cochlearis and Phompolyx sulcata. An indicator of moderate quality was Bosmina longirostris, while Daphnia longispina, Ascomorpha ovalis and Ascomorpha saltans were considered as indicators of good water quality. The data obtained suggest that zooplankton species can be used as a valuable tool to determine the water quality status and should be considered, in a near future, as one more of the BQE within the WFD metrics.