Understanding the biogeochemical response of tropical rivers to climate and socio-economic changes is a key scientific challenge. In such context, however, the hydrological functioning and transfer of carbon along tropical rivers – and the potential control of the tropical atmospheric circulation features – remain poorly documented and understood. To address this challenge, water, soil, sediment and suspended matter samples were collected in March and in October-November 2016 over three rivers basins from East Africa, located along a latitudinal transect across the Intertropical Convergence Zone and analysed for their chemical, isotopic and carbon compositions. Depending on internal characteristics of each basin, the three rivers have their own hydrological functioning identified during the low-water period. During the high-water period, all the rivers are mainly supplied by runoff and their isotopic signatures allow to reconstruct the origin of rains. The carbon originated from lateral inputs (rock weathering and soil erosion) depend on the geological geomorphological characteristics, on the hydro-climatological context, and on surrounding land use activities. In addition, the in situ primary production increases from upstream to downstream and provides an important part of the particulate organic carbon to the river. The carbon fluxes of the three basins are already impacted by climate and socio-economic patterns, and such impacts will most likely increase in the future. This will result on an increase of soil degradation and a decrease of carbon storage over the basins and an increase the production of organic carbon in streams by biological activities.