Future climate change is expected to impact the natural systems. This study used future climate data of general circulation models (GCMs) to investigate the impacts of climate change during the future period (2062–2095) relative to the historical period (1981–2014) on the hydrological system of the Minjiang river watershed, China. A previously calibrated soil and water assessment tool (SWAT) was employed to simulate the future hydrology under the impacts of changes in temperature, precipitation, and atmospheric CO2 concentration for four shared socioeconomic pathways (SSP 1, 2, 3, and 5) of the CMIP6. The study revealed that the impacts of increase in future temperature, i.e., increase in ET, and decrease in surface runoff, water, and sediment yield will be countered by increased atmospheric [CO2], and changes in the hydrological parameters in the future will be mostly associated to changes in precipitation. Data of the GCMs for all the SSPs predicts increase in precipitation of the watershed, which will cause increase in surface runoff, water yield, and sediment yield. Surface runoff will increase more in SSP 5 (47%), while sediment and water yield will increase more in SSP 1, by 33% and 23%, respectively. At the seasonal scale, water yield and surface runoff will increase more in autumn and winter in SSP 1, while in other scenarios, these parameters will increase more in the spring and summer seasons. Sediment yield will increase more in autumn in all scenarios. Similarly, the future climate change is predicted to impact the important parameters related to the flow regime of the Minjiang river, i.e., the frequency and peak of large floods (flows > 14,000 m3/s) will increase along the gradient of scenarios, i.e., more in SSP 5 followed by 3, 2, and 1, while duration will increase in SSP 5 and decrease in the other SSPs. The frequency and duration of extreme low flows will increase in SSP 5 while decrease in SSP 1. Moreover, peak of extreme low flows will decrease in all scenarios except SSP 1, in which it will increase. The study will improve the general understanding about the possible impacts of future climate change in the region and provide support for improving the management and protection of the watershed’s water and soil resources.