Here we analyze plankton communities of protists sampled across 38 saline and hypersaline water environments from arid climatic zones of South Urals of Russia and Crimea in light of environmental data using high-throughput 18S rDNA amplicon sequencing. We revealed significant differences in the taxonomic structure of eDNA biodiversity of protist communities depending on salinity, geographic location and pH. The protist communities demonstrated linear regression of richness and diversity and growth of percentage of unclassified Eukaryota (up to 43%) with the increasing of salinity. The obtained results provide insight into the taxonomy and diversity of protists in saline and hypersaline environments, and highlight the great potential for the discovery of new taxa due to the large number of unclassified 18S rDNA sequences.