A rapid groundwater recharge and circulation system has developed in Qaidam Basin, China. Stable H and O isotopes were monthly sampled in both river water and groundwater, and water table fluctuations were monitored over a complete seasonal cycle from dry-season to wet-season conditions in the Nalenggele River catchment in Qaidam Basin. The main goals are to demonstrate and explain rapid circulation in the groundwater system. A distinct seasonal fluctuation of the water table with associated stable isotopic variations can be observed in the alluvial-fluvial fan of the Nalenggele River catchment. During the wet season, replenishment of the aquifer results in a rising water table rises. The recharge mechanism appears to be related to the coincidence of several favorable hydrological conditions: an abundant recharge water source from summer precipitation and glacial-snow melt in the high Kunlun mountains, large-scale active faults, a volcanic crater and other macro-structures that act as favorable recharge conduits, the large hydraulic head from recharge areas to the alluvial-fluvial fan, and the presence of over 100 m of unconsolidated sand and gravel acting as the main aquifer. Warming climate is expected to increase precipitation and to accelerate melting of glaciers in the Kunlun Mountains, increasing recharge and leading to rapid rise in the water table in the alluvial-fluvial fan. Increased recharge in the future will provide water of improved quality to the Qaidam Basin, and will allow management of land in ways that reduce soil salinity and alkalinity.