The occurrence of hydrological extremes in the Amazon region and the associated sediment loss during rainfall events are key features in the global climate system. Climate extremes alter the sediment and carbon balance but the ecological consequences of such changes are poorly understood in this region. With the aim of examining the interactions between precipitation and landscape-scale controls of sediment export from the Amazon basin, we developed a parsimonious hydro-climatological model on a multi-year series (1997–2014) of sediment discharge data taken at the outlet of Óbidos (Brazil) watershed (the narrowest and swiftest part of the Amazon River). The calibrated model (correlation coefficient equal to 0.84) captured the sediment load variability of an independent dataset from a different watershed (the Magdalena River basin), and performed better than three alternative approaches. Our model captured the interdecadal variability and the long-term patterns of sediment export. In our reconstruction of yearly sediment discharge over 1859–2014, we observed that landscape erosion changes are mostly induced by single storm events, and result from coupled effects of droughts and storms over long time scales. By quantifying temporal variations in the sediment produced by weathering, this analysis enables a new understanding of the linkage between climate forcing and river response, which drives sediment dynamics in the Amazon basin.