Permafrost region subsurface organic carbon (OC) pools are a major component of the terrestrial carbon cycle and vulnerable to a warming climate. Thermokarst lagoons are an important transition stage with complex depositional histories during which permafrost and lacustrine carbon pools are transformed along eroding Arctic coasts. The effects of temperature and salinity changes during thermokarst lake to lagoon transitions on thaw history and lagoon deposits are understudied. We analyzed two 30-m-long sediment cores from two thermokarst lagoons on the Bykovsky Peninsula, Northeast Siberia, using sedimentological, geochronological, hydrochemical, and biogeochemical techniques. Using remote sensing we distinguished between a semi-closed and a nearly closed lagoon. We (1) characterized the depositional history, (2) studied the impact of marine inundation on ice-bearing permafrost and taliks, and (3) quantified the OC pools for different stages of thermokarst lagoons. Fluvial and former Yedoma deposits were found at depth between 30 and 8.5 m, while lake and lagoon deposits formed the upper layers. The electrical conductivity of the pore water indicated hypersaline conditions for the semi-closed lagoon (max: 108 mS/cm), while fresh to brackish conditions were observed beneath a 5 m-thick surface saline layer at the nearly closed lagoon. The deposits had a mean OC content of 15 ± 2 kg/m3, with higher values in the semi-closed lagoon. Based on the cores we estimated a total OC pool of 5.7 Mt-C for the first 30 m of sediment below five mapped lagoons on the Bykovsky Peninsula. Our results suggest that paleo river branches shaped the middle Pleistocene landscape followed by late Pleistocene Yedoma permafrost accumulation and early Holocene lake development. Afterward, lake drainage, marine flooding, and bedfast ice formation caused the saline enrichment of pore water, which led to cryotic talik development. We find that the OC-pool of Arctic lagoons may comprise a substantial inventory of partially thawed and partially refrozen OC, which is available for microbial degradation processes at the Arctic terrestrial-marine interface. Climate change in the Arctic leading to sea level rise, permafrost thaw, coastal erosion, and sea ice loss may increase the rate of thermokarst lagoon formation and thus increase the importance of lagoons as biogeochemical processors of former permafrost OC.

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane‐cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate‐rich marine water, altered the microbial methane‐cycling community. Anaerobic sulfate‐reducing ANME‐2a/2b methanotrophs dominated the sulfate‐rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non‐competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate‐poor sediments. CH4 concentrations in the freshwater‐influenced sediments averaged 1.34 ± 0.98 μmol g−1, with highly depleted δ13C‐CH4 values ranging from −89‰ to −70‰. In contrast, the sulfate‐affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011 ± 0.005 μmol g−1 with comparatively enriched δ13C‐CH4 values of −54‰ to −37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.

Subsea permafrost degradation was up to 170% faster below submerged thermokarst basins compared to submerged Yedoma remnants near shore• Re-worked permafrost beneath thermokarst basins adjacent to lagoons induces rapid offshore thaw• Along the assessed Arctic coastline, 54% of lagoons originated in thermokarst basins