Disturbance regimes including wildfire and permafrost thaw are intensifying across the boreal biome of northwestern Canada in response to climate change. Atmospheric exchanges of potent greenhouse gases such as water vapor, carbon dioxide (CO2), methane (CH4) affected by wildfire and permafrost thaw can potentially drive positive climate system feedbacks. The southern Taiga Plains ecozone is characterized by heterogenous boreal peatland complexes particularly vulnerable to intensifying disturbance regimes. Here, we present net fluxes of water vapor, CH4, and CO2 measured with the eddy covariance technique at three boreal peatland complexes with different disturbance histories near the southern limit of permafrost. Located in the sporadic permafrost zone, the two recently burned southern sites in Lutose, AB, acted as major CO2 sources. The two other sites mainly differed in permafrost extent, ranging from sporadic to discontinuous, and in peat plateau-to-wetland ratio and corresponding forest cover. CO2 uptake, CH4 emissions, and latent heat fluxes were larger at the sporadic than at the discontinuous permafrost site, whereas both, gross primary productivity and ecosystem respiration, as well as sensible heat fluxes were higher at the northern site. In conclusion, further permafrost thaw will only have negligible effects on the net ecosystem productivity of boreal peatlands in the Taiga Plains� discontinuous permafrost zone when compared to both, the positive net radiative forcing of increased CH4 emissions following permafrost thaw and the large CO2 losses post wildfire.