The Selenga River is the main tributary of Lake Baikal (Siberian, Russia). In 2015/2016, the water quality at previously identified contaminated hotspot regions in the lower Selenga River basin was evaluated using resident aquatic macroinvertebrate communities as bioindicators. Benthic macroinvertebrate communities within the Selenga River were found to be relatively sensitive to water pollution as was highlighted by three evaluated biotic indices:Average Score per Taxon (ASPT); Ephemeroptera-Plecoptera-Trichoptera density index (EPT); and Trent Biological Index (TBI). The human impact on the Selenga River basin water quality was evident due to the significant decrease of the biotic indices at several sample locations including downstream of the wastewater discharge point of Ulan-Ude city, in the Dzhida River downstream of the confluence of the Modonkul River, and especially in the Modonkul River near to the mining operations at Zakamensk. At the same time, our study revealed a high self-regeneration ability of the aquatic ecosystem throughout the basin; with resident benthic macroinvertebrate communities appearing to recover in both the Selenga River and the Dzhida River within two to five km downstream of the contamination source. The changes in the benthic communities at the Selenga delta sampling sites were shown to occur under the influence of natural factors such as hydrological conditions and benthic sediment type, which significantly changed from the upper to the lower regions of the delta. For the Selenga delta, a typology of benthic macroinvertebrate communities including a map of their spatial distribution is presented.