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A total of 413 diatom taxa were known for aquatic habitats of the Lena Delta Nature Reserve. We identified 385 taxa in 14 small tundra lakes near the reserve that significantly enriched the diatom diversity of the region (666 taxa including definitions to the genus level). Thus, the species composition of diatoms in the reserve and adjacent territories was increased by 278 species. We showed that the species of the genera Pinnularia (57) and Eunotia (51) have predominance at the family and generic levels. The index of intraspecific variability Ssp./Sp. for the lakes of the reserve was 1.11, and that for the lakes of the Tiksi region 1.14, which is typical for high-latitude and high-mountain communities. The number of rare or endangered species varied in different lakes from 1 to 10, totaling 42 species for the entire study area. Bioindication has shown that potentially threatened species prefer moderate temperatures, and slightly acidic or neutral environments free from organic pollution. A comparative analysis of the species composition of diatoms in the vicinity of the Lena Delta and other northern water bodies of Yakutia and the Arctic Islands showed that the species composition of each lake in the Arctic has a discernably different species distribution. The indicator characteristics show a certain response of the species composition of diatoms to changes in salinity, pH, and organic pollution. Regularities in the spatial distribution of diatoms in the study area were revealed in connection with the environmental variables of their habitat. Statistical mapping of diatom diversity data and bioindicators revealed a pronounced response to point pollution, and also let us assume the influence of summer northeast winds on species composition of the studied lake communities. We suggest that the high diversity inherent in the diatom lakes of the Tiksi coastal zone, which can even be updated in further studies, can be considered as a property of coastal biota inherent in ecotones. Since it is in the coastal Tiksi region that a surge in the number of species is observed, this region can be considered not only an ecotone, but also a hotspot of diatom diversity. The results of the study are important for developing the basis for monitoring biodiversity under the conditions of anthropogenic and climatic changes in the Arctic.