Climate, land use and human activity have an impact on the Qingshui River in Chongli County. The Soil and Water Assessment Tool (SWAT) was used to separately analyze the contributions of climate, land use and direct human activity on the discharge variations. The results indicated that human activity had been the dominant factor for the discharge decrease, while climate and land use change had a positive influence on the discharge increase. The contributions of these three factors were −56.24%, 38.59% and 5.17%, respectively. Moreover, on the seasonal scale, the impact of those factors was consistent with their impact on the annual scale. Human activity was the main factor for discharge decrease in the summer, the contribution accounting for −77.13%. Due to the over-extraction of groundwater for irrigation and use in the mining industry, the discharge showed a decreasing tendency, which has the potential to place stress on sustainable water use in the future. The result of the study may contribute to the optimization of water resource allocation and management.