Trend of precipitation and runoff in major Chinese rivers was calculated and compared in order to better quantify the hydrological processes and evaluate the role of human activities in changing river discharge. Records from 160 meteorological stations in China show that from 1951 to 2000 precipitation has increased (2%) in the south but decreased (4 to 11%) in the north. Hydrological data from 22 stations in five major Chinese rivers reveal that over the same period in the south runoff of Pearl River (Zhujiang) increased by 10% but Yangtze (Changjiang) runoff had little change. In the north flows in the Yellow (Huanghe), Liao and Songhua rivers decreased by 80%, 54% and 14%, respectively, all statistically significant based on Mann–Kendall trend analysis. Annual runoff in the Pearl and Yangtze rivers is correlated with basin-wide precipitation (R 2 of 0.72 and 0.81). Runoff from northern “deficit” rivers, however, was much lower than precipitation suggested, reflecting severe human impacts. Sub-basin analyses show that runoff in the “excess” southern Yangtze has increased more than precipitation would suggest, most likely indicating decreased water storage, decreased evapotranspiration, or both. In contrast, the marked decreases of runoff in northern sub-basins (including northern Yangtze and middle-lower Yellow) reflect drastically increased water consumption. The water crisis in northern China has been exacerbated by decreasing precipitation, doubling population and expanding water withdrawal, putting pressure on water management and economic development.