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Karst groundwater plays important roles as a water supply and in sustaining the biodiversity and ecosystems of the eastern Qinghai-Xizang Plateau. Owing to the stratigraphic structure, high tectonic activity, and changeable climate of the region, the recharge source, runoff path, and dynamic characteristics of karst groundwater are highly complex, which poses challenges with regard to the protection of water resources and ecology. This study identified the origin and flow processes of karst groundwater in the glacial lake area of the J