Based on the results of the integrated study of heavy metal concentrations and analysis of diatoms from subsurface bottom sediments, the contamination of the lower Shuya River and the effect of toxic substances on diatom complexes there were assessed. As heavy metal concentations rise, the percentage of halophilic organisms increases considerably, some mesohalobic species emerge and some planktonic diatoms of the genus Aulacoseira sp., ousted by the more tolerant species Aulacoseria granulata var. angustissima, Melosira varians, Navicula cryptocephala, N. rhyncocephala and N. viridula, and by many species of the genus Nitzschia sp., become less abundant or “drop out” from the community. Geochemical characteristics and diatom complexes were found to be related to various environmental factors such as river bed properties and the type of human-induced load.