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Abstract Understanding hydrological processes in the Source Area of the Yellow River (SAYR), Qinghai-Tibet Plateau, is vital for protection and management of groundwater and surface water resources in the region. In situ water measurements of exchange rates between surface water and groundwater are, however, hard to conduct because of the harsh natural conditions of the SAYR. We here present an indirect method using in situ 222Rn measurements to estimate groundwater discharge into rivers and lakes in the SAYR. 222Rn was measured in rivers, lakes, groundwater and springs during three sampling periods (2014–2016), and the results indicate large variability in the concentration of the isotope. The data also indicate decreasing 222Rn trends in groundwater in the cold season (the Feb-2015 sampling period) which may be linked to frequency of capturing 222Rn in the frozen ground caused by geocryogenic processes. In addition, permafrost spatial extent and freeze-thaw processes have strongly affected the hydrological conditions in the region. Highlights • 222Rn distribution in natural water of the Source Area of the Yellow River (SAYR). • 222Rn-based estimates of groundwater inflow rates to rivers and lakes in the SAYR. • Effects of frozen ground on 222Rn concentration in water. [ABSTRACT FROM AUTHOR]