<p>The Aral Sea is well known throughout the World as an inland lake disappearing due to unsustainable use of natural water resources for economic purposes. The degradation of the sea led to irreversible transformations of the ecosystem in the region and other destructive consequences. It has become a natural laboratory, allowing the study of the morphometric transformation of the properties of its waters under the influence of environmental conditions. This article is devoted to the study of temporal variability in the biogeochemical and physical characteristics with an emphasis on the metamorphosis of the ionic composition of the Aral waters and its individual water bodies (i.e., the Large and Small Aral Seas, Lakes Chernyshev and Tshchebas) in the period 1873 − 2022 based on newly obtained (2021 and 2022) and literature data. Periods of hydrochemical evolution are identified reflecting the order of salt deposition lasting for several years. The latest of these periods lasted from 2014 to 2022 waters in the salinity range of 126˗244 ‰. It was characterized by the <InlineEquation ID="IEq1"> <EquationSource Format="TEX">\({\text{SO}}_{4}^{2-}\)</EquationSource> <EquationSource Format="MATHML"><math> <msubsup> <mtext>SO</mtext> <mrow> <mn>4</mn> </mrow> <mrow> <mn>2</mn> <mo>-</mo> </mrow> </msubsup> </math></EquationSource> </InlineEquation>/Clˉ ratio of 0.31, while Mg²⁺/Na⁺ 0.34 and Ca²⁺/Na⁺ 0.02. Migration curves for the Aral Sea's water reflect the influence of a number of regional features on the formation of the ion-salt composition of waters was constructed. The biogeochemical features of the final stage of the Aral Sea are discussed using the example of the former bay and now lake Chernyshev. Its salinity of ~ 243 ‰ and the microbial community inhabiting it, along with the ionic composition, determines the properties of its waters.</p>