The source-to-sink system of a watershed is linked to tectonics, lithology, and climate, and includes erosion, sediment transport, and geomorphic change. Geological reconstructions of such systems are poorly understood, especially in arid and semi-arid regions with sparse geological evidence. Here, we reconstruct a watershed history from the Tarim River Basin since the Last Glacial Maximum (LGM) using river water geochemistry (including alkalinity and total dissolved solids) and sediment records from Lop Nur Salt Lake. Modern river geochemistry reveals that water availability and material supply control chemical weathering patterns, with significant spatiotemporal variations in sediment transport dynamics between hydrological seasons. Carbon proxies (total carbon, labile organic carbon, and related indicators) of borehole sediments suggest a wet environment in the Lop Nur area during the Holocene Megathermal, with a relatively high sediment carbon content. During the LGM, the climate was dry with lower sediment carbon. Geomorphological evidence can be used to further constrain sediment transport histories. We interpret millennial-scale paleorecords in the light of modern seasonal dynamics to reconstruct the evolution of the regional source-to-sink system. This analysis points to astronomical forcing as a key regulator of the relative contributions of sediment sources.