Ponds are active components of the global carbon cycle processing and emitting carbon dioxide and methane to the atmosphere. These common habitats frequently experience seasonal water table variations resulting in periodically air-exposed sediments. However, the influence of these events on both the system scale carbon balance and in-pond environmental conditions remains poorly studied. We took advantage of an extraordinarily warm and dry summer to quantify the CO2 efflux from air-exposed sediments and water surfaces in desiccating ponds on Öland, Sweden. Simultaneously, we modelled metabolism and measured environmental variables within the ponds. We found that air-exposed sediments had high CO2 effluxes greatly exceeding that from the water surfaces. Sediment water content influenced the temperature and strongly regulated the CO2 efflux gradually approaching zero as water evaporated. Within the desiccating ponds, respiration was generally higher than gross primary production, but was lower compared to the same ponds with higher water table. These findings highlight the role of periodically air-exposed pond sediments as sites of highly active carbon processes. Not only is this important for the system-scale carbon in ponds, but it may also influence the destiny of buried carbon in lakes subject to climate changes. The environmental conditions within desiccating ponds, most notably high water temperatures and poor oxygen conditions, further iterate the dynamics and extreme nature of ponds.