The transport of carbon from terrestrial ecosystems such as peatlands into rivers and out to the oceans plays an important role in the carbon cycle because it provides a link between the terrestrial and marine carbon cycles. Concentrations of dissolved organic carbon (DOC) and particulate organic carbon (POC) were analysed from the source to the mouth of the River Sebangau in Central Kalimantan, Indonesia during the dry and wet seasons in 2008/2009 and an annual total organic carbon (TOC) flux estimated. DOC concentrations were higher and POC concentrations lower in the wet season compared to the dry season. As seen in other tropical blackwater rivers, DOC concentration is consistently around 10 times greater than POC concentration. We estimate the annual TOC flux discharged to the Java Sea to be 0.46 Tg year−1 comprising of 93% (0.43 Tg) DOC and 7% (0.03 Tg) POC. This equates to a fluvial TOC loss flux per unit area over the entire Sebangau catchment of 88 g C m−2 yr−1. When extrapolating this TOC loss flux to the peat covered area of Indonesia (206 950 km2), we estimate a TOC loss of 18.2 Tg C yr−1 or ~10% of current estimates of the global annual riverine DOC discharge into the ocean.