There has been a marked decrease in river runoff in northern China recently, particularly from coal mining areas, but few studies have been able to quantify the factors influencing this phenomenon. Some methods to calculate the reasons for the river runoff decrease are urgently needed, and the degree to guide the river ecology restoration. Taking the Kuye River as an example, this study established a reference period (1960–1979) for a Soil and Water Assessment Tool (SWAT) model, and simulated the runoff changes and distribution. Then, the degree of influence of weather, water and soil conservation, industrial and domestic water consumption, and coal mining on river runoff during a recent period (1999–2010) was quantified. Finally, recent changes in runoff and its distribution were simulated with a modified SWAT model. The results show that in comparison to the reference period, for the recent period 21,987 × 104 m3 per year of runoff from the Kuye River was attributable to weather, while 8,840 × 104 m3, 5,346 × 104 m3 and 13,788 × 104 m3 was attributable to soil and water conservation measures, industrial and domestic water consumption, and coal mining respectively. The distribution of the runoff in the recent period was similar to that in the reference period, although its value was only half of the latter. These results can serve as an important reference for the ecological restoration of the Kuye River basin.