Sediment flows dynamics (erosion, transport and deposition) have been disrupted in South America (SA), a continent with the highest erosion and sediment transport rates globally. However, the magnitude and spatial distribution of the main drivers of changes have been poorly identified and explored. Here, we performed simulations using a hydrological-hydrodynamic-sediment model to comprehensively estimate the spatial and temporal sediment changes and trends in SA from 1984 to 2019. We found that 51% of the main SA rivers experienced significant changes in simulated sediment transport (QST) over this period, with 36% due to Amazon deforestation and river damming and 15% due to precipitation changes. We also estimated a 10% reduction in the average sediment delivery to the oceans. Deforestation was responsible for QST changes above 80% in some Amazon sites, and hydropower expansion led to a greater reduction of sediment flows (as high as 80-100%) in the Tocantins, Uruguay, Upper Paraná, lower São Francisco, Desaguadero, and Negro rivers. In addition, our results suggest that reservoirs built in the Amazon region in the last decade are also affecting sediment transport. Our modeling outputs provide unprecedented information about the status of sediment dynamics in SA, and a means to develop evidence-based strategies and transboundary policies related to continental-wide sediment dynamics and the conservation and restoration of ecosystems.