This data set is part of a larger data harmonization effort to make lake sediment core data machine readable and comparable. Here we standardized chironomid count data of sediment core PG2130, retrieved in 2013 from Lake Banya Toko (Yakutia, Russia) at 4.5 m water depth. The glacial lake Banya Toko is situated the deciduous forest mountain area. It lies at an elevation of ca. 902 m a.s.l. with a surface area of ca. 0.577 km2 and a maximum lake water depth of estimated 4.5 m. The 1.78 m 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). Chironomids have been counted using a light microscope at AWI Potsdam.