Due to the falling water level in the Aral Sea and Muynak Lake, the content of salts dissolved in the water has gradually increased, and toxic elements have been deposited at the lake’s bottom and subsequently washed into the Aral region by the river. Bacteria, archaea and fungi are crucial for the cycling of several important inorganic nutrients in soils. From 15 genera and 31 species of recovered microscopic filamentous fungi, a big group was melanized, of which most of them were also phytopathogenic. The second group consisted of keratinophilic species. Isolated bacteria mainly included members of the genera Arthrobacter, Bacillus, Massilia, Rhodococcus and Nocardiopsis. High-throughput sequencing analysis permitted a better view of the mycobiome and prokaryotic communities (comprising archaea). The cultivation and sequencing approaches were shown to be complementary. The aim of the work was to identify soil microorganisms, including the order Halobacteriales, and to discover the differences in species diversity depending on soil salinity and the presence of PTEs in soil.