Despite the key role of zooplankton communities in regulating the water quality of lentic ecosystems, they are absent from the list of biological elements of the Water Framework Directive (WFD) for the assessment of ecological status. Based on this, the present work was a case study that aimed to understand the relevance of zooplankton as a bioindicator for classifying the water quality of reservoirs. For one year and in each season, the water quality of the Torrão reservoir was assessed using the mandatory elements proposed by the WFD in the sampling year (second cycle) and the legislation currently applicable (third cycle). Additionally, zooplankton samples were collected to characterize the community dynamic. The water quality of the Torrão reservoir does not reach the WFD good ecological potential. Furthermore, with the updating of the criteria, the classification tends to get worse. Concerning the zooplankton, the occurrence of Cyclopoida and Bosmina are associated with lower water quality, as well as the collapse or low abundance of the Daphnia population, in the same periods. Low abundances of zooplankton are associated with better water quality, and the Shannon-Wiener diversity values decrease with the increase of the trophic state. High-efficiency feed filters and macrofiltrator organisms dominate the Torrão reservoir in all seasons, which is associated with low water quality. The Calanoida/Cyclopoida ratio shows a strong and negative association with the trophic state. The occurrence and abundance of species, Shannon-Wiener diversity, functional groups (high and low efficiency feed filters and macrofiltrators), and different ratios (large Cladocera/total Cladocera and Calanoida/Cyclopoida) are promising and valuable tools to determine the water quality status, and should be considered within the WFD metrics. Notwithstanding this, further research including reservoirs from different geographical areas with various trophic status and pressures must be analyzed.