The significant interest in the islands in the Russian Arctic has been in terms of available oil reserves, which determine the direction of economic development and associated environmental risks for this sector of the Arctic in the near future. Kotelny Island is the largest island of the New Siberian Islands Archipelago included in the protected zone of the Lena Delta Nature Reserve, which is located at 76° N, washed from the west by the Laptev Sea, washed from the east by the East Siberian Sea in a permafrost zone, and characterized by harsh climatic conditions defined by the northeast winds that prevail in vegetative season. January sees temperatures ranging from −32 to −35 °C, and July from +6 to +8 °C, which causes a short growing season. Samples were taken between August 3 and 8, 2018 in 12 freshwater bodies where 210 taxa were revealed. Aquatic communities were dominated by zygnematophycean and diatom algae, grouped in the basins of two rivers and associated with the position on the island’s landscape, which suggests the influence of cold north-east winds, leading to the avoidance of habitats in open and high places, which was revealed by statistical methods and also confirms the high individuality of taxa composition. Bioindication methods showed that water bodies are slightly alkaline, with low ion concentrations, with the presence of sulfides in low-lying habitats, and average saturation with organic matter. The mesotrophic status of the studied water bodies was evaluated through an assessment and the type of nutrition in the communities of algae and cyanobacteria indicates they formed there as true autotrophs, which corresponds to the status of a protected area and can serve as a reference level for monitoring anthropogenic impact.