Identifying changes in runoff and quantifying the impacts of climate change and human activities are of great significance for water resources planning and management in a river basin. In this study, an inflow series of the Three Gorges Reservoir observed from 1951 to 2016 is used to identify the trend and abrupt change point by using statistical methods. Based on the meteorological data, soil type data, and land use data during the same period, the Soil and Water Assessment Tool (SWAT) model is established to quantitatively attribute changes in the Three Gorges Reservoir inflow to climate change and human activities separately and discuss the differences between the two-stage method, which divides the whole study period into two stages to analyze the reasons for runoff evolution, and multi-stage method, which divides the whole study period into more stages to consider the temporal and spatial variation of land use/cover (LULC). The results show: (1) During the study period, a significant decrease is detected in the Three Gorges Reservoir inflow and the decrease rate is 7.7 km3
per ten years, annual total precipitation decreases by −13.5 mm per ten years, and annual average temperature increases by 0.1 °C per ten years. (2) Contribution of climate change and human activities is around 7:3. Climate change is the main reason for the decrease in the Three Gorges Reservoir inflow. (3) Results of stages in multi-stage method are different from the result of two-stage method. Accumulative results of multi-stage method and result of two-stage method are consistent. There are some changes in results of every stage, which are different from the accumulative results.
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