Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water supply. Climate variability and human activity had been identified as the two main reasons for the decrease in flow. Here, climate variability refers to changes in precipitation and temperature. Impact of human activity includes direct withdrawal of water (referred to as “direct abstraction” in this paper) from the river (primary) or groundwater and indirect impact due to man-made changes in land use and vegetation in the upstream of the reservoir. According to the historical record, “direct abstraction” from the upstream of the reservoir has increased significantly since 1984. The study period was split into two sub-periods, from 1956 to 1983 and from 1984 to 2005. Based on the historical record, annual runoff in the upstream catchment of Miyun Reservoir (i.e., inflow into the reservoir) had decreased from 90.3mm to 41.8mm for the two sub-periods, a decrease of 48.5mm. Over the same period, average annual “direct abstraction” increased from 2.2mm to 13.4mm, an increase of 11.2mm. The latter accounted for 23% (11.2mm/48.5mm) of the decrease in inflow into the reservoir. This study utilised: (1) a distributed hydrological model (geomorphology-based hydrological model, or GBHM) and (2) a climate elasticity model to conduct a quantitative assessment of the impact of climate variability and the indirect impact of human activity on the inflow into the reservoir. Simulation results of GBHM and the climate elasticity model showed that climate impact was accountable for about 55% and 51% of the decrease in reservoir inflow, respectively. The indirect impact of human activity (mainly man-made land use and vegetation changes) accounted for 18% of the decrease in reservoir inflow.