Clay subfractions (SFs) with particles size of 2–5, 0.6–2.0, 0.3–0.6, 0.2–0.3, and 0.1–0.2 μm of two shale samples (Upper Riphean Inzer Formation, South Urals) are studied using transmission electron microscopy, X-ray diffractometry (XRD), and U–Pb, Sm–Nd, Rb–Sr, and K–Ar methods. The SFs are composed of low-temperature 1Md illite; quartz, chlorite, and 2M1 illite are observed only in some coarse SFs. Irrespective of the size, the clay particles are equant. The standardized illite crystallinity indices (CIS) of all SFs are typical of the dia(cata)genesis zone. The CIS value increases, the I002/I001 ratio of XRD patterns decreases, and the K content and K/Rb ratio increase with decreasing particle size of the SFs from 2–5 to 0.1–0.2 μm. Leaching with 1N HCl and 1N NH4OAc and U–Pb, Sm–Nd, and Rb–Sr analysis of untreated SFs, leachate, and residue allowed us to study the isotope systematic of mixing in mobile and silicate material of shales. The 208U/204Pb and 87Rb/86Sr ratios of leachates are lower and the 147Sm/144Nd ratio is higher than those of residues. The leachates are also characterized by less radiogenic Pb and Sr and more radiogenic Nd relative to residues. With decreasing size of SF particles, the U, Pb, Sm, Nd, and Sr contents of leachates gently decrease and the Rb content increases. The 87Rb/86Sr and 87Sr/86Sr ratios of leachates of fine SFs are significantly higher, whereas their 238U/204Pb ratio is lower in comparison with coarse SFs. What is more, the data points of residues of various SFs occur along the mixing lines in the 87Rb/86Sr‒87Sr/86Sr and 1/86Sr‒87Sr/86Sr plots. The data points of corresponding leachates also form linear trends in 238U/204Pb‒206Pb/204Pb, 206Pb/204Pb‒207Pb/204Pb, 147Sm/144Nd‒143Nd/144Nd, and 87Rb/86Sr‒87Sr/86Sr coordinates. Apparent Rb–Sr ages calculated from slopes of “inner isochrons” (“leachochrons”) as well as K-Ar ages gradually decrease from 835–836 and 721–773 Ma, respectively, for SFs of 2–5 μm and to 572‒580 and 555‒580 Ma, respectively, for SFs of 0.1–0.2 μm. Thus, the XRD and isotopic data indicate that both clay and mobile shale constituents are mixtures at least of two components, and the silicate phase contains authigenic illites of various ages. First-generation illite abundant in the coarse SFs of 2–5 μm and 0.6–2.0 μm was formed immediately after the deposition of the Inzer sediments and its age of 803–836 Ma is consistent with stratigraphic age of the Inzer Formation. The formation of this illite was facilitated either by lithostatic burial or intense horizontal fluid flow caused by tectonic inversion in the eastern regions of the Uralian paleobasin. The age of the second-generation illite is 572–580 Ma; it was formed as a result of vertical movements or renovation of the composition of the pore fluids during deformations and metamorphism of the South Urals related to the evolution of the Beloretsk metamorphic complex.