Thermokarst lagoons, forming when thermokarst lakes are inundated by the sea, are an transition stage where terrestrial permafrost is introduced into the subsea realm. Here, permafrost and lacustrine carbon pools are transformed along Arctic coasts. During thaw previously frozen organic carbon can be converted into the greenhouse gases (GHG) carbon dioxide (CO2) and methane by microorganisms and leading to further climate warming. Especially for transition ecosystems like thermokarst lagoons it is largely unknown how GHG release is changing and whether thermokarst lagoons are a carbon source or sink. For getting a first glimpse of the consequences of saltwater inundation, we mimic the inundation of coastal permafrost in an experiment by incubating permafrost and thermokarst samples with artificial sea water under controlled conditions (4°C, dark, anaerobic) for 12 month. We used terrestrial samples from a 2.5 m high Yedoma outcrop, a thermokarst lake core, as well as samples from two neighboring thermokarst lagoons (a nearly-closed and a semi-closed) from the Bykovsky Peninsula, Northeast Siberia. By applying two different scenarios we aim to estimate (1) future GHG releases from newly formed Arctic lagoons by adding artificial seawater with a constant concentration and (2) the impact of increasing salinity on GHG production by incubating the samples under freshwater, brackish and marine conditions. Here we present (1) total organic carbon and dissolved organic carbon content for deep-drilled sediment cores (~ 30m) and (2) preliminary results on GHG production (methane and CO2) rates measured over 6 month. First results show that (1) GHG production is higher for inundated terrestrial sediments than for inundated lagoon sediments and (2) increasing salinity is favoring carbon dioxide production while methane production is low. In conclusion newly formed thermokarst lagoons, if upscaled to the thermokarst affected shorelines, are likely produce a significant amount of GHG under our experiment set-up.