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 PG2023, retrieved in 2010 from Lake Ozero Kyutyunda (Yakutia, Russia) at 2.9 m water depth. The thermokarst lake Ozero Kyutyunda is isituated in the coniferous forest area and has one outflow, one inflow and several smaller inflows. It lies at an elevation of ca. 56 m a.s.l. with a surface area of ca. 4.9 km2 and a maximum lake water depth of estimated 3.5 m. The 7.1 m sediment core was retrieved by a UWITEC 60mm piston corer during the RU-Land_2010_Lena 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 AXIO Scope.A1 light microscope with a Plan-Apochromat 100/1.4 Oil Ph3 objective at 1000x magnification.