Current warming, sea-level rise, coastal erosion and accelerated permafrost thaw is leading to increasing thermokarst lagoon formation along wide parts of the arctic coast. Entering seawater affects the temperature and salinity of former thermokarst lake taliks during their transition to the marine environment. Therefore, thermokarst lagoon formation is an important step in the process of mobilizing terrestrial permafrost carbon pools along rapidly changing Arctic coasts.This dataset presents results of sediment analyses (ice/water content, grain-size, bulk density, magnetic susceptibility), biogeochemical analyses (TC, TOC, TN, TOC/TN, d13C, d15N), pore water analyses (pH, electrical conductivity, DOC, stable water isotopes), freezing point calculations and radiocarbon dating of two sediment cores (> 30m long). The cores were taken at Uomullyakh Lagoon (PG2410) and Polar Fox Lagoon (PG2411) located at the Bykovsky Peninsula in April 2017.