BackgroundInvertebrates are important elements of aquatic ecosystems and play a crucial role in the transformation of matter and energy in continental water bodies. Communities of aquatic invertebrates are characterised by high sensitivity to pollution by nutrients and toxic substances and acidification of water bodies; they serve as good bioindicators of the quality of the aquatic environment and impacts on hydroecosystems. All hydrobionts participate in the processes of self-purification of water bodies.The presented dataset provides information on the aquatic invertebrate community of a large northern river. During 2018-2020, we collected data on changes in the quantitative indicators of the development of benthic and planktonic communities, as well as the species diversity of their fauna. The dataset combines information about the occurrence and abundance of benthic and planktonic invertebrates and summarises data of aquatic invertebrate species found in the Vychegda River in the zone of influence from the pulp and paper mill.New informationThe presented dataset is part of a monitoring programme of the river ecosystems in the production area of Mondi Syktyvkar JSC (the European North-East of Russia, Komi Republic). The dataset describes the structure of benthic invertebrate and plankton communities in the Northern Dvina River Basin. The data on the finding and abundance of large taxa of aquatic invertebrates and species of some groups: Oligochaeta, Cladocera, Copepoda, Rotifera, Ephemeroptera, Plecoptera and Trichoptera are presented. In total, the resource includes 8720 findings of invertebrates, of which 6041 are for zoobenthos organisms and 2679 for zooplankton organisms.