Summary1. We relate invertebrate assemblages to direct measurements of near-bed hydraulic conditions that integrate the complex three-dimensional structure of flow close to the bottom.2. We sampled invertebrate taxa from a Mediterranean River along a spatial gradient of increasing shear stress in two seasons (spring and autumn) with different hydrological conditions. We used a recently described ordination technique, Outlying Mean Index (OMI) analysis, to study the response of stream invertebrates to near-bed hydraulic parameters.3. The distribution of nearly 70% of the taxa collected was significantly related to the hydraulic parameters assessed. In both seasons, shear stress and Froude number were the most important hydraulic parameters whereas substratum particle size and bed roughness had less influence. Most of the 31 taxa collected in both seasons had a higher OMI (an index showing the deviation between the mean environmental conditions used by a taxon and the mean environmental conditions used by a theoretical taxon uniformly distributed across the studied gradient) in autumn (when flow was greater) and were found in samples with high shear stress and high Froude number. This suggests that benthic invertebrates changed their preferences according to flow conditions.4. Taxon richness declined with increased shear stress during lower flow in spring. Finally, and agreeing with previous results, the proportion of filter feeders and collector-gatherers was inversely related to shear stress.5. Our results are a first step towards better habitat suitability models that could inform management decisions.