Climate change may have profound impacts on the maintenance of peatlands and surface water systems in the sub-humid western Boreal Plain (WBP) of Northwestern Canada. Wetlands in the WBP, whereas significant carbon stocks are sensitive to changes in climate, because in most years potential evapotranspiration (ET) exceeds precipitation. In this study, a dynamic closed chamber technique was used to examine the relative midday (10:00–16:00 h) growing season (April–October) contributions of heterotrophic and autotrophic respiration (Rtot) and moss photosynthesis (gross ecosystem production, GEP) to net ecosystem exchange (NEE) of CO2 at the soil surface of different degrees of spruce forest canopy cover and microtopography (lawn and depression) in two peatland–pond complexes in the WBP, north–central Alberta, Canada. Results demonstrate that Sphagnum lawns showed the greatest amount of uptake, and dominant surface cover plant communities (Sphagnum and feather mosses) were associated more with canopy cover and incident radiation (photosynthetically active radiation, PAR) than microclimate and hydrology. Although microclimate and hydrology varied spatially, no major changes in plant communities were observed across microtopographic gradients (lawns and depression). Differences in NEE with hydrology and microclimate were observed between microtopographic units (depression and lawns), but this was not consistent with surface cover plant community types, which makes generalized fluxes in this landscape particularly challenging. Copyright © 2010 John Wiley & Sons, Ltd.