A lack of appropriate proxies has traditionally hampered our ability to distinguish riverine organic carbon (OC) sources at the landscape scale. However, the dissection of C4 grasslands by C3-enriched riparian vegetation, and the distinct carbon stable isotope signature (δ13C) of these two photosynthetic pathways, provides a unique setting to assess the relative contribution of riparian and more distant sources to riverine C pools. Here, we compared δ13C signatures of bulk sub-basin vegetation (δ13CVEG) with those of riverine OC pools for a wide range of sites within two contrasting river basins in Madagascar. Although C3-derived carbon dominated in the eastern Rianala catchment, consistent with the dominant vegetation, we found that in the C4-dominated Betsiboka basin, riverine OC is disproportionately sourced from the C3-enriched riparian fringe, irrespective of climatic season, even though δ13CVEG estimates suggest as much as 96% of vegetation cover in some Betsiboka sub-basins may be accounted for by C4 biomass. For example, δ13C values for river bed OC were on average 6.9 ± 2.7‰ depleted in 13C compared to paired estimates of δ13CVEG. The disconnection of the wider C4-dominated basin is considered the primary driver of the under-representation of C4-derived C within riverine OC pools in the Betsiboka basin, although combustion of grassland biomass by fire is likely a subsidiary constraint on the quantity of terrestrial organic matter available for export to these streams and rivers. Our findings carry implications for the use of sedimentary δ13C signatures as proxies for past forest-grassland distribution and climate, as the C4 component may be considerably underestimated due to its disconnection from riverine OC pools.Electronic supplementary materialThe online version of this article (doi:10.1007/s10021-014-9772-6) contains supplementary material, which is available to authorized users.