Baseflow is the portion of streamflow that comes from groundwater storage and other delayed sources, and is an integral part of the hydrological process. It is crucial to ensure the ecological water volume of rivers or lakes by choosing a scientific and reasonable baseflow separation method and identifying the driving factors that affect the change of baseflow. Therefore, the original achievement and objective of this study were to further contribute to the literature to fill the gap in the knowledge of how to analyse the impacts of climate change and human activities on baseflow more reasonably and comprehensively. The Bai River Basin of Miyun Reservoir was selected as a case study in this paper. The comparison and selection of methods were discussed, and the evolution characteristics of baseflow and its influencing factors were analyzed. Finally, the corresponding management guidance was given. The baseflow separation results of local minimum method, single parameter digital filter method and recursive digital filter were compared based on the measured streamflow data and related meteorological data from the Zhangjiafen Hydrological Station in the Bai River Basin from 1967 to 2012. Driving factors that affect baseflow changes were also identified from two aspects of climate change and human activities. The results showed the recursive digital filter method had better application stability in the Bai River Basin compared to other methods. The baseflow had a relatively high contribution rate to the river streamflow (BFI >0.65) in the Bai River Basin of Miyun Reservoir. The amount of annual baseflow of the Bai River Basin had a very significant decreasing trend (P<0.01) from 1967 to 2012, while the annual baseflow index remained unchange. The baseflow sequence of the Bai River Basin had abrupt changes in 1980 and 1999, respectively. The abrupt change of the baseflow sequence in 1999 was mainly affected by the precipitation (climate change). The abrupt change in 1980 was not dominated by precipitation, but mainly affected by other factors, such as human activities. Therefore, in the future, it is necessary to rationally conserve the source of baseflow, and deepen the understanding and research on the rule of streamflow evolution, especially the impact of climate change and human activities on water resources. It will be of great significance to the safety of water supply in Beijing and the optimal allocation and management of regional water resources. This study enhances our understanding of the relative roles of climate variations and human activities on baseflow.