To investigate the reaction of the zooplankton community to improving water quality in the Schelde estuary, we studied the relationship between rotifer species distribution and environmental factors, and the feasibility of using a coarser level of taxonomic resolution. Fifty-two taxa, belonging to 26 genera, were identified, including 22 taxa new for the Schelde. Brachionus calyciflorus, Keratella cochlearis and B. angularis were the most abundant species. The highest diversity and abundances were observed in the freshwater reach. Redundancy analyses (RDA) showed that the main environmental factors explaining rotifer distribution were chlorinity and seasonal factors (discharge levels, cyclopoid abundance). Analysis carried out with data at the species and the genus level gave similar ordination plots, but the positioning of a genus relative to environmental factors did not always adequately represent the associations between the various species within the genus and environmental factors. Similar patterns in space and time were observed using taxonomic richness and diversity indices for analyses at species or genus level. Thus, in the context of the restoration of the Schelde estuary, the identification of rotifer species is very informative, but not essential for detecting important ecological associations.