Data obtained from 14 years of monthly samplings (1996e2009) were used to investigate the response of the crustacean zooplankton community to improving water quality in the Scheldt estuary. A strong reduction of poor water quality indicators, such as NH4þ and BOD5, as well as an increase in oxygen and in chlorophyll a concentrations were observed during the study period. During the study period, important changes were observed in the zooplankton community composition and spatial distribution. From 2007 onwards, most of the calanoid population, previously mainly found in the brackish water reach of the estuary, moved to the freshwater, where they reached higher abundances than previously observed. Simultaneously, cyclopoids populations strongly decreased in freshwater while cladocerans did not change their abundance, except during years with high chlorophyll a concentrations. Redundancy analyses (RDA) showed that the variability within the calanoid population can be explained by the improvement in water quality. Variability within the cyclopoids and cladoceran community is mainly explained by chlorinity and chlorophyll a concentrations. Their presence in the most polluted upstream area until 2007 suggests they are more tolerant to poor water quality than calanoids. Several hypotheses to explain the disappearance of cyclopoids after the move of calanoids to the freshwater are presented and discussed.