In the last decades, hydromorphological degradation of rivers has gained more attention in river management, stressing the importance of understanding the links between hydromorphology and aquatic assemblages. The present study investigated general patterns in the response of benthic invertebrate assemblages to single morphological features along naturally diversified Slovenian rivers. The whole gradient of local habitat quality (river habitat quality, RHQ) and habitat modification (river habitat modification, RHM) features, according to the Slovenian hydromorphological assessment method, was covered. Regional natural characteristics explained the low share of RHQ and RHM variability, indicating nonregional presence of morphological features. The analysis identified predominant flow and predominant channel substrate as the most important RHQ features. We found that in contrast to RHQ features, RHM features had low explanatory power. These results suggest a weaker response of benthic invertebrate assemblages to the physical alteration itself than to the effect that the alteration exerts on habitat quality features. Variance partitioning among three environmental variable groups revealed predominantly independent effects (69%) on benthic assemblages, mostly on account of regional natural characteristics (30%) and RHQ features (31%). As benthic invertebrate assemblages are adapted to the former natural conditions, a similar modification may result in different effects with regard to regional natural differences. Therefore, the low proportion of variability, explained by RHM features, might be the consequence of joint dataset from different regions. Our study gives general implications for river management, but in order to more clearly define the significance of particular modification features, we suggest further analysis within more homogeneously defined habitats that encompass regional natural characteristics.