Study region: The Qinghai Lake Basin, Qinghai-Tibetan Plateau. The Qinghai Lake is the largest inland saltwater lake in China. Study focus: Significant increase in runoff into the Qinghai Lake has been reported; however, the relationship between frozen soil changes and runoff remains poorly understood. This study investigated the temporal and spatial variations in frozen soil and associate effects on streamflow and soil moisture in the study region by a distributed eco-hydrological model. New hydrological insights: The results illustrate that the coverage of permafrost decreased by about 13% from 1971 to 2015, and permafrost degradation mainly occurred in the elevation interval of 3600-4200 m. The maximum frozen depth averaged in the seasonally frozen ground significantly decreased by 0.06 m/10a, while the active layer thickness averaged in the permafrost enhanced by 0.02 m/10a. Permafrost degradation caused enhanced soil liquid water storage and an increase in freezing season runoff. The increase in runoff in the thawing season was dominated by changes in precipitation. The results suggest that frozen soil degradation altered the seasonal flow regime, leading to lags in the monthly runoff peak, and it increased the base flow and reduced the thawing season runoff. This offset of the competing impacts of frozen soil changes in different seasons led to a negative effect on annual runoff. This study provides new understandings of cryospheric hydrological responses to climate change.