When highly degraded, lowland thermokarst landscapes are flooded by the sea, and thermokarst lagoons, lakes, and the sea become connected with each other, complex lagoon systems are formed. Consequently, a natural gradient of marine submergence age and connectivity emerges within the system with older, well-connected lagoons closer to the sea, and younger, less connected lagoons further inland. The dataset presents the cumulative greenhouse gas production and daily production rates from 7 lagoons of variing sea connectivity and permafrost and active layer as endmembers. In detail sediment of active layer (AL) and permafrost (PF) from a soil pit located on the lowland of Reindeer Island (RI21-P2-AL, RI21-P2-PF), a thermokarst lake (RI21-05 (TKL05)), a limited open lagoon (LAG13), two semi-open lagoons (LAG04; LAG14), two mostly open lagoons (LAG03; LAG16) and two open lagoons (LAG07; LAG12). 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).