The response of permafrost to submergence can vary between ice-rich late Pleistocene deposits and the thermokarst basins that thawed out during the Holocene. We hypothesize that inundated Alases offshore thaw faster than submerged Yedoma. To test this hypothesis, we estimated depths to the top of ice-bearing permafrost offshore of the Bykovsky Peninsula in northeast Siberia using electrical resistivity surveys. The surveys traversed submerged lagoon deposits, drained and refrozen Alas deposits, and undisturbed Yedoma from the coastline to 373 m offshore. While the permafrost degradation rates of the submerged Yedoma were in the range of similar sites, the submerged Alas permafrost degradation rates were up to 170% faster. Given the abundance of thermokarst basins and lakes along parts of the Arctic coastline, its effect on subsea permafrost degradation must be similarly prevalent. Remote sensing analyses suggest that 54% of lagoons wider than 500 m originated in thermokarst basins.