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 PG2360, retrieved in 2016 from Lake Bety (Yakutia, Russia) at 1.5 m water depth. The thermokarst lake Bety is a small thermkarst lake in the coniferous forest area and has one outflow and three inflows. It lies at an elevation of ca. 160 m a.s.l. with a surface area of ca. 0.66 km2 and a maximum lake water depth of estimated 1.5 m. The 2.31 m sediment core was retrieved by a Russian peat corer during the RU-Land_2016_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). Diatoms have been counted using a ZEISS light microsocope at 1000x magnification at AWI Potsdam, and valve concentration was detected using microspheres.