A considerable part of the global carbon budget is stored in the Arctic permafrost landscapes. Several studies suggest that lakes and ponds play a key role in the carbon turnover of these ecosystems as they are considered to be favourable paths of carbon exchange between surface and atmosphere. The direction and strength of the carbon fluxes from Arctic lakes is controlled by a variety of physical and biochemical processes whose climate interactions are complex and still poorly understood. In some Arctic regions the fractional area of lakes and ponds can be as large as 25% highlighting the importance of water bodies in the Arctic ecosystems. Our long-term studies on the energy balance of a typical Arctic lake landscape reveal that the seasonal freeze-thaw dynamic is highly sensitive to small variations in the winter time radiation budget and the subsurface heat flux, especially at shallow ponds. The time required to completely freeze the water body including the subjacent bottom sediments can vary up to several months. This implies that the period of unfrozen ponds, during which biological activity is favourable, highly depends on factors such as the winter time cloudiness and snow cover. Hence, the close interaction between the winter time surface energy balance and biological processes might strongly affect the production and storage of green house gases of Arctic landscapes. This potential climate feedback mechanism is even more important as small water bodies are usually below the spatial resolution of remote sensing products. Therefore, they are not included in landscape classifications used in recent estimates of the global carbon budget or climate models. Nevertheless, small water bodies can make up a considerable percentage of the tundra surface comparable in size to the area occupied by large (thermokarst) lakes. Further investigation on the role of small water bodies appears to be mandatory for a better understanding of the Arctic carbon balance.