The eco-morphodynamic activity of large tropical rivers in South and Central America is analyzed to quantify the carbon flux from riparian vegetation to inland waters. We carried out a multi-temporal analysis of satellite data for all the largest rivers in the Neotropics (i.e, width > 200 m) in the period 2000–2019, at 30 m spatial resolution. We developed a quantification of a highly efficient Carbon Pump mechanism. River morphodynamics is shown to drive carbon export from the riparian zone and to promote net primary production by an integrated process through floodplain rejuvenation and colonization. This pumping mechanism alone is shown to account for 8.9 million tons/year of carbon mobilization in these tropical rivers. We identify signatures of the fluvial eco-morphological activity that provide proxies for the carbon mobilization capability associated with river activity. We discuss river migration—carbon mobilization nexus and effects on the carbon intensity of planned hydroelectric dams in the Neotropics. We recommend that future carbon-oriented water policies on these rivers include a similar analysis.