The increase in extreme climate events such as flooding and droughts predicted by the general circulation models (GCMs) is expected to significantly affect hydrological processes, erosive dynamics, and their associated nonpoint source (NPS) pollution, resulting in a major challenge to water availability for human life and ecosystems. Using the Hydrological Simulation Program–Fortran model, we evaluated the synergistic effects of droughts and rainfall events on hydrology and water quality in an upstream catchment of the Miyun Reservoir based on the outputs of five GCMs. It showed substantial increases in air temperature, precipitation intensity, frequency of heavy rains and rainstorms, and drought duration, as well as sediment and nutrient loads in the RCP 8.5 scenario. Sustained droughts followed by intense precipitation could cause complex interactions and mobilize accumulated sediment, nutrients and other pollutants into surface water that pose substantial risks to the drinking water security, with the comprehensive effects of soil water content, antecedent drought duration, precipitation amount and intensity, and other climate characteristics, although the effects varied greatly under different rainfall patterns. The Methods and findings of this study evidence the synergistic impacts of droughts and heavy rainfall on watershed system and the significant effects of initial soil moisture conditions on water quantity and quality, and help to guide a robust adaptive management system for future drinking water supply.