These datasets describe a 31.5 m long sediment core taken from beneath thermokarst lake Goltsovoye Lake (71.74515 N, 129.30217 E) on the Bykovsky Peninsula, northeastern Siberia. The thermokarst lake was 510 cm deep. Here, we report the depths from the ice surface as well as from the sediment surface.The first dataset presents biogeochemical and hydrochemical parameters of sediment core PG2412. Biogeochemical analyses include total nitrogen (TN) content, total carbon (TC) content, total organic carbon (TOC) content and stable carbon isotopes (δ13C). δ13C was measured for samples with TOC > 0.1 wt %. Hydrochemical parameters include pore water content, pH and electrical conductivity (EC).The second dataset presents the grain size distribution of sediment core PG2412. The fraction > 1 mm is not included.The third dataset presents the radiocarbon ages from samples from sediment core PG2412. Calibrated and rounded calibrated ages are presented. Calibrations were performed according to Stuiver et al. (2017) using CALIB 7.1 software and the IntCal13 calibration curve.The fourth dataset presents the n-alkane data from samples from sediment core PG2412. Concentrations of n-alkanes in the range n-C23 to n-C33 are given in µg/g sediment and µg/g TOC. From the n-alkane concentrations, we calculated the following indices: average chain length (ACL), carbon preference index (CPI), odd-over-even predominance (OEP), n-Alkane ratio, aquatic plant proxy (Paq) and terrestrial plant proxy (Pwax).