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Reconstruction of hydrological fluctuations in arid regions has proven challenging due to a lack of reliable chronologic constraints on sparse geological archives. The aim of this study was to establish an independent record of hydrologic changes in the hyper-arid Tarim Basin (TB; northwest China) with high spatiotemporal resolution. We present comprehensive radiocarbon and tree-ring data sets of subfossilized plant remains in the TB compiled from geomorphological investigations of the paleochannels of the Tarim River (TR), the longest endorheic river in China, crossing the world's second-largest shifting sand desert. Results show that the late medieval configuration of the TR basin was characterized by enhanced hydrological connectivity, as indicated by the formation of significant riparian forests in the desert regions at ca. 1170 CE. A distinct low-flow interval (ca. 1500-1650 CE) is identified for the first time, refining the period of a wetter-than-present TB. The present-day organization of streams in the lower TR was proto-formed after the dry period, possibly led by episodic flood-induced diversion. Our study describes the centennial-scale dynamics in the TR flow over the past millennium, offering a robust long-term context for hydrological assessment in the extensive drylands of the Asian interior. [ABSTRACT FROM AUTHOR]