Benthic macroinvertebrates are an important indicator of river health. However, their response upon water quality development downstream the pollution outlets considerably depends on the environmental habitat characteristics. Three successive stretches, each of them providing three different mesohabitats in stillwater (S), torrential (T) and riparian (R) zones were selected for evaluation of the impact of altered metapotamal river bed morphology (channelization) and chemical determinants of water quality on the Upper Elbe River. In downstream direction, the stretches are separated by weirs and characterized as a low polluted low modified natural stream (N), a low polluted channelized stream (C) and a channelized polluted stream (CP). Altogether, 111 benthic macroinvertebrate taxa were recorded in the Pardubice hotspot between Němčice and Přelouč. Despite different levels of stream bed and water quality degradation, micro- and mesohabitat characteristics appeared to be the most important factors determining the diversity of macrozoobenthos in riffle (substrate size structure) and in shoreline (macrophyte community composition and structure) mesohabitats. The diversity of macroinvertebrate communities was highest in riparian mesohabitats compared to stillwater and torrential ones. Saprobic indices increased in downstream direction, thus indicating the decline of water quality.