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.This 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).