Recent climate change has caused an increase in warming-driven erosion and sediment transport processes on the Tibetan Plateau (TP). Yet a lack of measurements hinders our understanding of basin-scale sediment dynamics and associated spatiotemporal changes. Here, using satellite-based estimates of suspended sediment, we reconstruct the quantitative history and patterns of erosion and sediment transport in major headwater basins from 1986 to 2021. Out of 13 warming-affected headwater regions, 63% of the rivers have experienced significant increases in sediment flux. Despite such intensified erosion, we find that 30% of the total suspended sediment flux has been temporarily deposited within rivers. Our findings reveal a pronounced spatiotemporal heterogeneity within and across basins. The recurrent fluctuations in erosion-deposition patterns within river channels not only result in the underestimation of erosion magnitude but also drive continuous transformations in valley morphology, thereby endangering local ecosystems, landscape stability, and infrastructure project safety.