This data set is part of a larger data harmonization effort to make lake sediment core data machine readable and comparable. Here we standardized X-ray fluorescence line scanning (XRF)-based element data of sediment core PG2133, retrieved in 2013 from Lake Bolshoe Toko (Yakutia, Russia) at 26 m water depth. The glacial lake Bolshoe Toko is in the deciduous forest mountain area. It lies at an elevation of ca. 919 m a.s.l. with a surface area of ca. 83.243 km2 and a maximum lake water depth of estimated 72.5 m. The 3.75 m sediment core was retrieved by a UWITEC piston corer during the RU-Land_2013_Yakutia expedition of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI, Germany, Potsdam) in cooperation with the North Eastern Federal State University (NEFU, Russia, Yakutsk). The downcore elemental composition was measured using an AVAATECH x-ray fluorescence core scanner at AWI Bremerhaven.