AbstractA tropical ombrotrophic peatland ecosystem is one of the largest terrestrial carbon stores. Flux rates of carbon dioxide (CO2) and methane (CH4) were studied at various peat water table depths in a mixed‐type peat swamp forest floor in Central Kalimantan, Indonesia. Temporary gas fluxes on microtopographically differing hummock and hollow peat surfaces were combined with peat water table data to produce annual cumulative flux estimates. Hummocks formed mainly from living and dead tree roots and decaying debris maintained a relatively steady CO2 emission rate regardless of the water table position in peat. In nearly vegetation‐free hollows, CO2 emission rates were progressively smaller as the water table rose towards the peat surface. Methane emissions from the peat surface remained small and were detected only in water‐saturated peat. By applying long‐term peat water table data, annual gas emissions from the peat swamp forest floor were estimated to be 3493±316 g CO2 m−2 and less than 1.36±0.57 g CH4 m−2. On the basis of the carbon emitted, CO2 is clearly a more important greenhouse gas than CH4. CO2 emissions from peat are the highest during the dry season, when the oxic peat layer is at its thickest because of water table lowering.