Accurate determination of carbon balances in heterogeneous ecosystems often requires the extrapolation of point based measurements. The ground resolution (pixel size) of the extrapolation base, e.g. a land-cover map, might thus influence the calculated carbon balance, in particular if biogeochemical hot spots are small in size. In this paper, we test the effects of varying ground resolution on the calculated carbon balance of a boreal peatland consisting of hummocks (dry), lawns (intermediate) and flarks (wet surfaces). The generalizations in lower resolution imagery led to biased area estimates for individual micro-site types. While areas of lawns and hummocks were stable below a threshold resolution of ~60 cm, the maximum of the flark area was located at resolutions below 25 cm and was then decreasing with coarsening resolution. Using a resolution of 100 cm instead of 6 cm led to an overestimation of total CO<sub>2</sub> uptake of the studied peatland area (approximately 14 600 m<sup>2</sup>) of ~5% and an underestimation of total CH<sub>4</sub> emission of ~6%. To accurately determine the surface area of scattered and small-sized micro-site types in heterogeneous ecosystems (e.g. flarks in peatlands), a minimum ground resolution appears necessary. In our case this leads to a recommended resolution of 25 cm, which can be derived by conventional airborne imagery. The usage of high resolution imagery from commercial satellites, e.g. Quickbird, however, is likely to underestimate the surface area of biogeochemical hot spots. It is important to note that the observed resolution effect on the carbon balance estimates can be much stronger for other ecosystems than for the investigated peatland. In the investigated peatland the relative hot spot area of the flarks is very small and their hot spot characteristics with respect to CH<sub>4</sub> and CO<sub>2</sub> fluxes is rather modest
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