The impact of water quality, landuse, hydromorphology on benthic macroinvertebrate assemblages of the Bednja River was studied. 20 longitudinally distributed study sites were sampled using the AQEM multihabitat sampling method resulting in the collection and identification of 193,638 benthic macroinvertebrate individuals belonging to 259 taxa. Diversity and assemblage composition greatly varied between the study sites and microhabitats. There was no grouping of communities based on river type. . Two separate assessment systems for hydromorphological modification were tested on the same river reach. RHS scores explained more variation in assemblages than EN 15843:2010 scores. The two assessment systems gave differing results regarding the extent of hydromorphological modification, but never the less had highly correlated subscores. Several water quality and nutrient parameters followed a longitudinal gradient but hydromorphological modification did not, showing that degradation is present along the entire course of the river. Benthic invertebrate diversity and functional metrics generally poorly correlated with hydromorphological modification scores. Assemblages on technolithal differed from but those on natural lithal substrate. The high diversity supported by technolithal is explained by the presence of periphyton. The correlation of hydromorphological modification with predators is due to Hydrachnidia which are associated with technolithal. The response gradient shows an improvement in Ecological Status with increased HQA scores.