The dataset presents the greenhouse gas production (CO2 and CH4) from sediment of a terrestrial permafrost outcrop (Byk14-A-1; 71.85175°N, 129.350883°E), the thermokarst lake Goltsovoye (PG2412 (TKL), 71.74515°N, 129.30217°E), the nearly-closed Polar Fox Lagoon (PG2411 (LAG1), 71.743056°N, 129.337778°E) and the semi-open Uomullyakh Lagoon (PG2410-1 (LAG1), 71.730833°N, 129.2725°E). We incubated the samples anaerobically at 4 °C under fresh (c=0 g/L), brackish (c=13g/L) and marine (36g/L) conditions for one year and measured carbon dioxide (CO2) and methane (CH4) concentrations regularly in a 250 µL subsample using gas chromatography with an Agilent GC 7890A equipped with an Agilent HP-PLOT Q column. Cumulative CO2 and CH4 concentrations and production rates per day are given over time for all samples with three replicates each per gram of dry weight and normalised to gram of soil organic carbon (SOC).