The zooplankton fauna of the Zeeschelde estuary (Belgium) was investigated over 10 months by means of monthly sampling. Canonical Correspondence Analysis (CCA) was used to relate the species distribution to environmental factors. The variation in the species data was significantly (P < 0.05) related to a set of 10 environmental variables (chlorinity, NH4+, temperature, PO4-P-, DW, Chl a and Chl b, NO2-N, NO3-N and pH). The main spatial and seasonal gradients were associated with chlorinity and temperature respectively. The brackish water zone was dominated by the calanoid Eurytemora affinis in spring, succeeded by Acartia tonsa and mysid species during summer. In the freshwater transect, cyclopoids dominated, together with several cladoceran species. Thermophilic cyclopoid species (Thermocyclops oithonoides, Th. Crassus and Mesocyclops leuckarti) occurred during periods of maximal temperature. The cyclopoids Acanthocyclops robustus, Paracyclops poppei and Cyclops vicinus, the cladocerans Daphnia longispina, Chydorus sphaericus and Bosmina longirostris together with the numerically dominant rotifers, oligochaetes, nematodes and juvenile copepods seemed little affected by environmental gradients.