Abstract. Tropical peat-draining rivers are known as potentially large sources of carbon dioxide (CO2) to the atmosphere due to the high loads of carbon they receive from surrounding soils. However, not many seasonally resolved data are available, limiting our understanding of these systems. We report the first measurements of carbon dioxide partial pressure (pCO2) in the Rajang River and Estuary, the longest river in Malaysia. The Rajang River catchment is characterized by extensive peat deposits found in the delta region, and by human impact such as logging, land use and river damming. pCO2 averaged 2540±189 µatm during the wet season and 2350±301 µatm during the dry season. Using three different parameterizations for the gas transfer velocity, calculated CO2 fluxes to the atmosphere were 1.5 (0.5–2.0) g C m−2 d−1 (mean, minimum – maximum) during the wet season and 1.7 (0.6–2.6) g C m−2 d−1 during the dry season. This is at the low end of reported values for Southeast Asian peat-draining rivers, but similar to values reported for Southeast Asian rivers that do not flow through peat deposits. In the Rajang River, peatlands probably do not contribute much to the CO2 flux due to the proximity of the peatlands to the coast, which limits the opportunity for degradation of organic C during transport. Thus, we suggest that peat coverage is, by itself, insufficient as the sole predictor of CO2 emissions from peat-draining rivers, and that other factors, like the spatial distribution of peat in the catchment and pH, also need to be considered.