Tropical peatlands, which coexist with swamp forests, have accumulated vast amounts of carbon as soil organic matter. Since the 1970s, however, deforestation and drainage have progressed on an enormous scale. In addition, El Niño and Southern Oscillation (ENSO) drought and large-scale fires, which grow larger under the drought condition, are accelerating peatland devastation. That devastation enhances decomposition of soil organic matter and increases the carbon release to the atmosphere as CO2. This phenomenon suggests that tropical peatlands have already become a large CO2 source, but related quantitative information is limited. Therefore, we evaluated the CO2 balance of a tropical peat swamp forest in Central Kalimantan, Indonesia, using 3 years of CO2 fluxes measured using the eddy covariance technique from 2002 through 2004. The forest was disturbed by drainage; consequently, groundwater level (GL) was reduced. The net ecosystem CO2 production (NEP) measurements showed seasonal variation, which was slightly positive or almost zero in the early dry season, and most-negative late in the dry season or early the rainy season. This seasonality is attributable to the seasonal pattern of climate, tree phenology and fires. Slightly positive NEP resulted from smaller ecosystem respiration (RE) and larger gross primary production (GPP) under conditions of high photosynthetic photon flux density (PPFD) and large leaf area index (LAI). The most-negative NEP resulted from smaller GPP and larger RE. The smaller GPP was related to high vapor pressure deficit (VPD), small LAI and low PPFD because of smoke from fires. The larger RE was related to low GL. Annual NEP values were estimated respectively as −602, −382 and −313 g C m−2 yr−1 for 2002, 2003 and 2004. These negative NEP values show that the tropical peat swamp forest, disturbed by drainage, functioned as a CO2 source. That source intensity was highest in 2002, an ENSO year, mainly because of low PPFD caused by dense smoke emitted from large fires.