The dataset comprises the main geochemical characteristics of purified lake sediment samples from Lake Bolshoye Shchuchye, in the Polar Ural based on EDS and stable isotope data. Moreover, core segment (column A), composite depth (in cm; column B); calibrated age (in cal ka BP; column C) are given. Details on coring and age model are given in Lenz et al. (2021) Energy-Dispersive X-ray Spectroscopy (EDS) was carried out with a scanning electron microscope (SEM) at the German Research Centre for Geosciences (GFZ Potsdam, Germany) to assess contamination of all diatom samples (following Chapligin et al., 2012). Three replicate analyses were carried out with an excited-area size with a radius of ~200 μm at an acceleration voltage of 20.0 kV. All detectable elements were normalized to 100% weight. The results were expressed as weight percentages (in %) and displayed as oxides: SiO2 content (%); Al2O3 content (%); Na2O content (%); MgO content (%); K2O content (%); CaO content (%); MnO content (%); FeO content (%): Total sum (%) of the purified sediment sample (columns D to L). Details are given in Meyer et al. (2022) The diatom oxygen isotope composition (δ18Odiatom) from lacustrine sediments helps tracing the hydrological and climate dynamics in individual lake catchments. The oxygen isotope data has been generated in the ISOLAB Facility Potsdam including all d18Odiatom values (all in ‰ vs. VSMOW). The measured δ18O values (δ18Omeas), the standard deviation (SD) and number of replicates (N) are given (columns M to O), as well as the calculated contamination (ccont; in %) and δ18O values corrected for contamination (δ18Ocorr) (columns P to Q). The details of the contamination correction and isotope analytics are given in Meyer et al. (2022)