The macrocrustacean community of brackish polder waters in Flanders was investigated based on a twenty year survey comprising 430 biological samples taken at 218 different locations. A clear shift in the gammarid community could be observed. After its introduction, the alien Gammarus tigrinus, originating from North America, reached high abundances and became widely spread in the polder waters within a few years. Simultaneously, a decrease in the prevalence of the indigenous brackish water gammarids G. duebeni and G. zaddachi occurred. However, at the same time a decrease in the salinity of the polder waters also was observed. Uni- and multivariate data analysis revealed a clear difference in the environmental preferences of G. tigrinus, G. duebeni, and G. zaddachi. The alien species preferred lower salinities, lower orthophosphate concentrations, and a higher oxygen concentration compared to the two indigenous species. Besides the decrease in prevalence of the native gammarids, a decrease was also observed in prevalence of two other indigenous brackish water crustaceans: Palaemonetes varians and Neomysis integer. It appears that the decrease in salinity is the most important factor causing the decline of the indigenous gammarids and not the introduction of the alien G. tigrinus.