The relationship between microcrustacean assemblage structure and flow habitat was investigated in 9 streams with differing hydraulic characteristics. A series of partial canonical correspondence analyses was used to relate species abundances of microcrustacea to geographical chemical hydraulic, and seasonal variables. Once the influence of geography (latitude) on species distributions was removed, the environmental variables accounted for almost 38% of the variation in the combined (all seasons) data set. Circumneutral streams had greater species richness and higher abundance of cosmopolitan species than more acidic streams. The microcrustacean assemblages were distinguished further on the basis of stream hydraulic character Previous research had categorised the 9 streams into Type I, II, or III depending on the fraction of stream bed retaining low shear stress at high discharge (declining from Types I to III). Taxa that are largely epibenthic in habit tended to be most abundant in Type I streams. These taxa may use as habitat the extensive low shear stress areas present in these streams, enabling their survival even at high discharge Conversely, taxa that are largely interstitial in habit tended to be most abundant in Type II and III streams. The distribution of interstitial taxa may reflect conditions within the substratum rather than at the surface The differences in microcrustacean assemblage structure were largely species-specific; the Harpacticoida were the only group to show a consistent pattern in relation to stream hydraulics.