It is important to understand carbon (C) dynamics in terrestrial and coastal ecosystems in order to develop a strategy to control carbon dioxide effluxes. However, the factors determining concentrations of riverine carbon are still largely unknown, especially in Southeast Asia. We investigated the spatial distribution of dissolved and particulate organic carbon (DOC and POC, respectively) and suspended sediment (SS) concentrations in the Kemena and Tatau rivers of Sarawak, Malaysia, in 2011, 2012 and 2013. There are large variations in DOC and POC concentrations in both rivers and their spatial patterns also differ. DOC concentrations did not vary over the sampling years and mainly depended on the distribution of tropical peatland within the watershed. Excitation-emission matrix (EEM) fluorescence spectroscopy with parallel factor analysis showed that DOC supplied from peatland is distinctive though the fluorescence characteristics do not change with the creation of plantations. SS and POC concentrations were slightly higher in logged forests and plantations and significantly higher in main rivers than in intact forests. The results suggest that DOC concentrations are geographically controlled by peatland distribution, while intensive plantation development and the resultant soil disturbance can cause an increase in terrestrial POC discharges to the ocean.