We present integrated mineralogical, geochemical, and palynological data for Late Pleistocene–Holocene bottom sediments of Lake Arakhlei located in the Beklemishev tectonic basin in the southern Vitim Plateau (central Transbaikalia). The sediment samples were studied by X-ray diffractometry (XRD), Fourier-transform infrared (FTIR) spectroscopy, laser particle sizing, spore–pollen analysis, radiocarbon (14C AMS) dating, and XRF spectrometry. The cored 128 cm long section of lake sediments consists of two units: One is composed mainly of layered silicates (illite–smectite, illite, chlorite, chlorite–smectite, muscovite, and kaolinite) and organic matter (OM) but no carbonates from 0 to 80 cm and the other contains authigenic Ca–Mg carbonates (up to 30%) of Mg-calcite and excess-Ca dolomite from 80 to 128 cm. The sediments also contain a rare mineral weddellite CaC2O4⋅2H2O discovered for the first time in Transbaikalian lakes. The evolution of Lake Arakhlei and its drainage basin comprised four stages, with pollen zones that mark the Late Pleistocene and Holocene climate history of the Beklemishev basin. The reconstructed history of Lake Arakhlei for the past ~ 15,500 years followed general climatic changes in the Northern Hemisphere. Thus, integrated research, including detailed analysis of mineral components and spore–pollen assemblages in lake sediments, is a workable tool for studying climatic controls of continental sedimentation.