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 16-KP-03-L10_Long_1, retrieved in 2016 from Lake Nutenvut (Chukotka, Russia). The glacial lake Nutenvut is in an exorheic basin in the tundra-taiga transition zone. It lies at an elevation of ca. 654 m a.s.l. with a surface area of ca. 9.2 km2 and a maximum lake water depth of estimated 60 m. The 1.26 m sediment core was retrieved by a UWITEC hammer action gravity corer during the RU-Land_2016_Keperveem 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.