Measurement of the spatial variability of CH4 emissions and net CO2 ecosystem exchange were made in a boreal peatland in northern Sweden in the summers of 1992 and 1993. Variability was monitored at the microscale (hummocks and hollows), mesoscale (ridges, lawns and pools), and macroscale (landforms) to assess the role of peatland topography on the magnitude and variability of the fluxes. The general trend is for topographically lower areas, such as hollows, pools, or peatland margins, to have higher CH4 emissions and lower CO2 uptake than the adjacent topographically higher areas such as hummocks, ridges, and plateaus. However, the greatest difference occurs at the microtopographic scale because the maximum differences in water table position and temperature occur at the microscale. The CH4 flux at the margins of the peatland was three to four times greater than that observed at the central plateau sites. Net CO2 uptake was also greatest at the margin sites. A combined meso‐macro topographic model (MMF) was used to estimate the total peatland CH4 and CO2 exchange. The model indicates that a failure to measure the exchange of carbon from peatland pools can result in a large overestimate of the total peatland NEE and therefore carbon accumulation rates.