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Fluvial geomorphology proposes the methodology of cognition and assessment of the riverine landscape and points to the possibilities of exploitation of its results in hydrobiological research. Habitat structure of two reaches of the Drietomica brook (Biele Karpaty Mts, Slovakia) was assesed at level of morphological and morphohydraulic units in the sense of the River Morphology Hierarchical Classification (RMHC)). Physical habitats were described by flow hydraulics and substrate properties as directly measured variables (current velocity, depth, substrate size) and related variables (flow type, Froude and Reynolds numbers). According to the shear stress (expressed by Fr and Re), the morphological units were divided into two main groups -with low shear stress -pools, glides, edgewaters, bar nooks and bars; with high shear stress -riffles, runs, rapids and scours; characterized also by different Ephemeroptera, Plecoptera and Trichoptera (EPT) communities. The EPT communities were analyzed in relation to the morphological, hydraulic and substrate characteristics of the stream channel. The main environmental gradient responsible for the variation in EPT fauna was found using Principal Component Analysis and was related to gradient of flow in term of current velocity and other hydraulic attributes covered by Fr and Re numbers. The EPT communities (by means of abundance, feeding types, current, microhabitat and zonation preferences) showed preferences for different morphological units, flow type and current velocity. Depth and substrate grain size showed only weak relation to EPT communities.