This data set describes times series of diatom species counts, organic matter measurements including total carbon TC, total organic carbon TOC, nitrogen N, stable carbon isotopes d13C, and mercury Hg concentrations in four short cores (PG2133, PG2139, PG2203, PG2208 from Lake Bolshoe Toko, eastern Siberia. These short core have been dated using 210Pb and 137Cs methods covering the transition zone of the industrialization until 2013 CE. Methods are provided in the associated paper (Biskaborn et al. 2021).