In this study, the runoff changes and their attribution from 1960 to 2012 for Wuding River basin and its two tributaries, Hailiutu River in the wind-sand region and Dali River in the Loess hilly region, were analyzed. The future trends in runoff changes in the three rivers were also predicted. The results revealed that runoff of the Wuding River, Hailiutu River, and Dali rivers decreased significantly during the period of 1960 to 2012, although the annual rainfall in the three river basins did not change significantly during this period. The annual evapotranspiration of the Wuding River and Hailiu River was nearly constant, while the annual evapotranspiration of Dali River has increased significantly since the late 1990s. Abrupt change points of runoff were detected in 1979 and 1996 of Wuding River, 1971 and 1990 of Hailiutu River, and 1971 of Dali Rive, respectively. Human activities accounted for approximately 50% of the runoff reduction in Dali River from 1972 to 2012 and 44.4% in Hailiutu River from 1972 to 1990, 82.4% from 1991 to 2012, respectively. In the future, the annual runoff of the Wuding River and its two tributaries, Dalihe River and Hailiutu River would continue to decline. Attribution analysis revealed that large-scale soil and water conservation measures are the main reasons for sediment and runoff reduction in Dali River. The water conservancy projects' constructions and farmland irrigation are the main reasons for runoff reduction in Hailiutu River. Therefore, it is necessary to optimize the existing vegetation pattern to reduce evapotranspiration and decelerate the decrease rate of runoff in the Dali River basin. In the Hailiutu River basin, it is necessary to conduct "Grain to Green", to control the irrigation area of farmland, improve the efficiency of irrigation water, and reduce the amount of used irrigation water, at the same time to increase the water conservation capacity as well.