been identified as a major large-scale factor affecting stonefly community composition in streams [4], whereas important medium-and small-scale factors can include stream size, substratum and water quality.A windstorm in November 2004 flattened 12,000 hectares of forest along southerly oriented slopes of the Tatra Mountains, and also sections of brook catchment areas. Since this windstorm caused large scale destruction of mature forests over such an extensive area, including that of the riverine landscape of the brooks, this unique natural disturbance provided a great opportunity for ecological research [5,6].The Plecoptera are one of the best bioindicators of human disturbances in streams [7]. Within the benthic macroinvertebrates, stoneflies are selected for evaluation of long-term changes [8]. Stoneflies are useful biological indicators of river quality, reflecting stream degradation, land use, and deforestation [9,10].Ambühl [11] and Egglishaw [12] relate the distribution of several macroinvertebrate species to current water velocity and substrata. Egglishaw [12] showed that, even in what was apparently a fairly uniform stretch of riffle, i.e. a length of short shallow coarse-bedded stream, the densities of several benthic species varied greatly by site and were correlated with the substrata type. The riverbed gave ground for the interactive linkages between the fluvial-morphological, hydrological-hydraulic and sedimentation processes in space (lateral, longitudinal and vertical dimensions) and in time [13,14]. The result is a dynamic structure of morphological units (microhabitats), which form the basis of the structure and organization of biotic associations. The effects of flow on organisms can be expressed by the complex variable, shear stress [15]. Also, a correlation between average current velocity and hydraulic conditions near the substrate has been described [16], which indicates that average velocity has a significant relationship to conditions on the substratum and biota. Substrate heterogeneity is created by disturbance and variability in physical conditions [17]. Heterogeneity produces patchiness in environmental conditions [18], including food availability, which in turn results in high species diversity in benthic invertebrates.Abstract: Stonefly samples were collected from disturbed and undisturbed tributaries of the Tatra Mountains streams (the West Carpathians). In the autumn, at stable low discharge, the total density of stoneflies was significantly higher in the undisturbed streams. Microhabitats such as macrolithal (boulders), mesolithal (stones) and moss had higher stonefly density. Taxa of different species or genera have different demands for microhabitats. Very narrow spatial niches were found for the genera Rhabdiopteryx, Protonemura and Perlodes. The spatial niche overlap was low between the genera Rhabdiopteryx and Brachyptera, but was high between species of the Protonemura and Leucra genera. The highest biodiversity of stoneflies was on coarser substrata (except boulders) and m...