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The Yellow River flow has decreased substantially in recent decades, and the river often dried up in the lower reach and failed to reach the sea. Climate change and human disruption have been suggested as major causes of the flow reduction, but quantification of their relative contribution is challenging due to limited instrumental records and disturbance by dams. Here we use a basin-wide tree ring network to reconstruct the Yellow River flow for the past 1,200 years and show that the flow exhibits marked amplitude variations that are closely coupled to the hydrological mean state swings at multidecadal to centennial timescales. Recent flow should have increased to the highest level of the past 1,200 years if there were no human disruption. However, human activities have caused a loss of nearly half of natural flow since the late 1960s and are the main culprit for recent downstream flow reduction.