The Tienshan Mountains, with its status as "water tower", is the main water source and ecological barrier in Central Asia. The rapid warming affected precipitation amounts and fraction as well as the original glacier/snowmelt water processes, thereby affecting the runoff and water storage. The ratio of snowfall to precipitation (S/P) experienced a downward trend, along with a shift from snow to rain. Spatially, the snow cover area in Middle Tienshan Mountains decreased significantly, while that in West Tienshan Mountains increased slightly. Approximately 97.52% of glaciers in the Tienshan Mountains showed a retreating trend, which was especially obvious in the North and East Tienshan Mountains. River runoff responds in a complex way to changes in climate and cryosphere. It appears that catchments with a higher fraction of glacierized area showed mainly increasing runoff trends, while river basins with less or no glacierization exhibited large variations in the observed runoff changes. The total water storage in the Tienshan Mountains also experienced a significant decreasing trend in Middle and East Tienshan Mountains, but a slight decreasing trend in West Tienshan Mountains, totally at an average rate of -3.72 mm/a. In future, water storage levels are expected to show deficits for the next half-century.