This dataset comprises the elemental distributions from high-resolution X-ray fluorescence (XRF) scanning from sediment core EN20001, retrieved from Lake Khamra, SW Yakutia. XRF was performed at the Bundesanstalt für Geowissenschaften und Rohstoffe (BGR), Berlin, Germany. The resolution of measurement for the whole core (0-1080cm) is 1 cm, except for the part 659-729 cm (where 0.5 cm was applied, to check for fine laminations).This study was additionally supported by a short-term grant (not numbered) from AWI Graduate School (POLMAR), and PhD Completion Scholarship (not numbered) provided by University of Potsdam.