This data set is part of a larger data harmonization effort to make lake sediment core data machine readable and comparable. Here we standardized diatom count data of sediment core PG2201, retrieved in 2013 from Lake Malaya Chabyda (Yakutia, Russia), located approximately 15 km southwest of the City of Yakutsk, at 2 m water depth. Lake Ulakhan Chabyda (Event: PG2315) discharges into Lake Malaya Chabyda during times of high water. The thermokarst lake Malaya Chabyda is situated in the coniferous forest area and has one outflow and one inflow. It lies at an elevation of ca. 192 m a.s.l. with a surface area of ca. 0.18 km2 and a maximum lake water depth of estimated 3 m. The sediment core was retrieved by a Russian peat 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). Eight overlapping sediment cores, representing an approximately 6.6 m–long composite sequence were collected on March 24, 2013. Two parallel drilling holes, approximately 1 m apart, were used alternatingly to obtain core sections which overlap by approximately 20 cm. Diatoms have been counted using a ZEISS light microsocope at 1000x magnification at AWI Potsdam.