In modern conditions of climate change and increased anthropogenic pressure on aquatic ecosystems, the study of the diversity of organisms in the Arctic has become a top priority. Our study continues a series of studies on the biodiversity of Arctic rivers. Using innovative methods, such as ecological mapping, statistics, and bioindication, we identify environmental factors that influence phytoplankton diversity in the river basin under study. For the Anabar Arctic River, an increase in the diversity of phytoplankton was found to the north towards the mouth of the river, which is associated with an increase in turbidity from industrial discharges. A weak effect of organic pollution and toxic effects associated with existing settlements have been identified, but it has been established that natural processes of self-purification take place in the studied Arctic River. Among 210 species of phytoplankton, an increase in the diversity of chrysophytes in the northern direction was revealed, consistent with the intensification of severe Arctic climatic conditions. Since the study region is characterized by increased diamond mining, we recommend continuing to monitor phytoplankton, track changes in the Anabar River ecosystem, and expand such observations to other Arctic rivers.