As the dominant mode of deforestation in the Congo Basin, shifting agriculture is expected to increase with the projected four-fold population growth for the region by 2,100. To assess how this land-use change will affect the export of carbon (C) to rivers in a typical lowland forest ecosystem, we studied paired watersheds near Kisangani, Democratic Republic of the Congo. Two streams, one draining an intact forest (Forest) and one draining an agricultural landscape (Ag), were gauged, equipped with sensors, and sampled fortnightly for one year. Annual average specific discharge was 1.4 mm d−1 (+76%) higher in the Ag compared to the Forest. Average annual dissolved organic C (DOC) and particulate organic C (POC) concentrations were 5.2 mg L−1 (+163%) and 1.3 mg L−1 (+81%) higher in the Ag stream, which, along with the higher discharge, resulted in 8.3 (+410%) and 2.4 g C m−2 yr−1 (+97%) larger C yields, respectively. Baseflow dissolved inorganic carbon, carbon dioxide, and methane yields were also higher in the Ag stream. Despite the higher yields of organic C (OC), the composition of OC did not differ significantly. Carbon to nitrogen ratios, along with isotopic signatures, revealed that both streams contained young, semi-degraded organic matter derived from C3 vegetation. Correspondingly, biodegradable DOC (BDOC) proportions did not differ between the streams, although the Ag stream yielded more total BDOC. These results show that agricultural land-use likely exports a greater proportion of Net Primary Productivity (NPP) to aquatic ecosystems, which may affect both C storage in soils and the proportion of gross PP that is ultimately respired.