The spatial spring distribution of Eurytemora affinis (adults and C5) in the Scheldt estuary (Belgium) brackish and freshwater reacheswas studied in between 1996 and 2007. The bulk of the E. affinis population being generally situated in the brackish water reach (salinity > 0.5); we studied which environmental factors are responsible for its recent sporadic occurrence in the freshwater estuarine reach. Using PLS analysis, it is shown that its presence upstream is limited by a sufficient oxygen concentration (>4mg l-1) that is associated with temperature. Not only are the environmental conditions in the upstream zone important, but also the frequent presence of an O2 minimum zone in the mid-estuary (O2 min < 1.3mg l-1) seems to block the movement of the downstream E. affinis population in an upstream direction. Occasionally, the bulk of the population is however situated upstream. During these periods, high E. affinis abundancewas also observed in the Durme tributary. Our findings suggest the possibility to use E. affinis as an “indicator” species ofwaterquality, but also lead us to stress the necessity to consider conditions over the entire estuary when studying restoration effects, not exclusively in the zone of interest.