Adverse effects of future climate change on water supply system are of concern. High turbidity caused by abrupt flood, and drought caused by continuous dry days are the major risks. To assess such risks, a comprehensive method to simulate hydrology with high spatiotemporal resolution should be developed. In this study, a series of methods from parameter estimation to future simulation using the Soil and Water Assessment Tool (SWAT) was demonstrated for Sagami Dam reservoir, which is a typical water supply reservoir in Japan. A proposed parameter calibration method by optimizing percent bias followed by optimizing Nash–Sutcliffe efficiency gave good performance of model prediction of the daily average reservoir inflow in the past. Using this model, the changes in inflow under expected climate change were simulated. Three predicted daily climates by the Model for Interdisciplinary Research on Climate version 5 (MIROC5) under three representative concentration pathways, i.e., RCP 2.6, 4.5, and 8.5, in 2081–2100 were used for the simulation, whereas observed daily climate during 1981–2000 was used as the past reference. The risks were discussed by considering their seasonality, indicating increases in flood and drought in June and July, and in February and April, respectively.