The paper presents original authors' data on the O, H, C, S, and Sr isotopic composition of water and sediments from the basins into which the Aral Sea split after its catastrophic shoaling: Chernyshev Bay (CB), the basin of the Great Aral in the north, Lake Tshchebas (LT), and Minor Sea (MS). The data indicate that the δ18О, δD, δ13C, and δ34S of the water correlate with the mineralization (S) of the basins (as of 2014): for CB, S = 135.6‰, δ18О = 4.8 ± 0.1‰, δD = 5 ± 2‰, δ13C (dissolved inorganic carbon, DIC) = 3.5 ± 0.1‰, δ34S = 14.5‰; for LT, S = 83.8‰, δ18О = 2.0 ± 0.1‰, δD =–13.5 ± 1.5‰, δ13C = 2.0 ± 0.1‰, δ34S = 14.2‰; and for MS, S = 9.2‰, δ18О =–2.0 ± 0.1‰, δD =–29 ± 1‰, δ13C =–0.5 ± 0.5‰, δ34S = 13.1‰. The oxygen and hydrogen isotopic composition of the groundwaters are similar to those in MS and principally different from the artesian waters fed by atmospheric precipitation. The mineralization, δ13С, and δ34S of the groundwaters broadly vary, reflecting interaction with the host rocks. The average δ13С values of the shell and detrital carbonates sampled at the modern dried off zones of the basins are similar: 0.8 ± 0.8‰ for CB, 0.8 ± 1.4‰ for LT, and –0.4 ± 0.3‰ for MS. The oxygen isotopic composition of the carbonates varies much more broadly, and the average values are as follows: 34.2 ± 0.2‰ for CB, 32.0 ± 2.2‰ for LT, and 28.2 ± 0.9‰ for MS. These values correlate with the δ18O of the water of the corresponding basins. The carbonate cement of the Late Eocene sandstone of the Chengan Formation, which makes up the wave-cut terrace at CB, has anomalously low δ13С up to –38.5‰, suggesting origin near a submarine methane seep. The δ34S of the mirabilite and gypsum (11.0 to 16.6‰) from the bottom sediments and young dried off zone also decrease from CB to MS in response to increasing content of sulfates brought by the Syr-Darya River (δ34S = 9.1 to 9.9‰) and weakening sulfate reduction. The 87Sr/86Sr ratio in the water and carbonates of the Aral basins do not differ, within the analytical error, and is 0.70914 ± 0.00003 on average. This value indicate that the dominant Sr source of the Aral Sea is Mesozoic–Cenozoic carbonate rocks. The Rb–Sr systems of the silicate component of the bottom silt (which is likely dominated by eolian sediments) of MS and LT plot on the Т = 160 ± 5 Ma, I0 = 0.7091 ± 0.0001, pseudochron. The Rb–Sr systems of CB are less ordered, and the silt is likely a mixture of eolian and alluvial sediments.