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 core scanning (XRF)-based element data of sediment core 16-KP-04-L19_Long_2 retrieved in 2016 in Lake Rauchuagytgyn (Chukotka, Russia). Lake Rauchuagytgyn is situated within the Rauchua mountain valley in the north-western Anadyr Mountains of Chukotka (Arctic Siberia). It lies at an elevation of ca. 625 m a.s.l. with a surface area of ca. 6.1 km2 and maximum water depth of 36 m. The 3 m sediment core 16-KP-04-L19 was retrieved by a modified hammer UWITEC gravity corer deployed from a catamaran 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). It was collected within 3 m PVC plastic liners, cut into 1-m pieces until further analyses. Sediment cores were tranported to AWI and one half scanned for elemental data by X-ray fluorescence (XRF) analysis at the Federal Institute for Geosciences and Natural Resources (BGR), Berlin, Germany.