Tropical peatlands have accumulated huge soil carbon over millennia. However, the carbon pool is presently disturbed on a large scale by land development and management, and consequently has become vulnerable. Peat degradation occurs most rapidly and massively in Indonesia, because of fires, drainage, and deforestation of swamp forests coexisting with tropical peat. Peat burning releases carbon dioxide (CO2) intensively but occasionally, whereas drainage increases CO2 emission steadily through the acceleration of aerobic peat decomposition. Therefore, tropical peatlands present the threat of switching from a carbon sink to a carbon source to the atmosphere. However, the ecosystem-scale carbon exchange is still not known in tropical peatlands. A long-term field experiment in Central Kalimantan, Indonesia showed that tropical peat ecosystems, including a relatively intact peat swamp forest with little drainage (UF), a drained swamp forest (DF), and a drained burnt swamp forest (DB), functioned as net carbon sources. Mean annual net ecosystem CO2 exchange (NEE) (± a standard deviation) for 4 years from July 2004 to July 2008 was 174 ± 203, 328 ± 204 and 499 ± 72 gC m−2 yr−1, respectively, for the UF, DF, and DB sites. The carbon emissions increased according to disturbance degrees. We found that the carbon balance of each ecosystem was chiefly controlled by groundwater level (GWL). The NEE showed a linear relationship with GWL on an annual basis. The relationships suggest that annual CO2 emissions increase by 79–238 gC m−2 every 0.1 m of GWL lowering probably because of the enhancement of oxidative peat decomposition. In addition, CO2 uptake by vegetation photosynthesis was reduced by shading due to dense smoke from peat fires ignited accidentally or for agricultural practices. Our results may indicate that tropical peatland ecosystems are no longer a carbon sink under the pressure of human activities.