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 PG1972, retrieved in 2009 from Lake Bezrybnoe (Lena Delta, Russia) at 4.7 m water depth. The thermokarst lake Bezrybnoe is small basin in tundra region and has one outflow and three inflows. It lies at an elevation of ca. 6 m a.s.l. with a surface area of ca. 0.77 km2 and a maximum lake water depth of estimated 5.3 m. The 1.08 m sediment core was retrieved by a UWITEC hammer action gravity corer (60mm) during the RU-Land_2009_Lena-transect 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). Diatoms have been counted using a ZEISS light microsocope at 1000x magnification at AWI Potsdam.