Better understanding the fate of the atmospheric carbon (C) captured by plant photosynthesis is essential to improve natural C flux modelling. Soils are considered as the major terrestrial bioreactor and repository of plant C, whereas channel networks of floodplain rivers collect and transport, throughout the aquatic continuum, a significant part of plant primary production until its export through outgassing or sequestration in marine sediments. Here, we show that river meandering in forested floodplains is a crucial and widely overlooked Earth surface process promoting C fluxes from the atmosphere to the aquatic continuum, via the floodplain vegetation. Over a recent period of 35 years (1984–2019), we quantified those C fluxes in one of the most active meandering rivers on Earth, the Ucayali River, Peru, South America. We used map time series combined with above-ground forest C data to derive the amount of C that is annually captured by the growing floodplain vegetation within the active meander belt, as well as exported to the aquatic continuum by lateral channel erosion. We found that the annual building and erosion of forested floodplain areas was nearly balanced over time with 19.0±7.7×103 ha−1 yr−1 and 19.8±6.7×103 ha−1 yr−1, respectively. While growing forests within the active meander belt annually captured 0.01±0.05×106 Mg C yr−1, lateral channel erosion provided the nearly 100-fold amount of C to the river channel and its streamflow, i.e. 0.9±0.4×106 Mg C yr−1. Our findings revealed that the migration of the Ucayali River channel provided nearly 10-times more lignified C per unit area to the aquatic continuum (44.7±21.4 Mg C ha−1 yr−1) than non-meandering central Amazonian floodplains do. Together, these findings point to the importance of quantifying the overall contribution of meandering rivers to natural C fluxes worldwide.