Construction of tunnels and caverns affects not only groundwater flow and groundwater table over a wide area but also runoff in some cases. Changes in groundwater and runoff conditions during and after such construction should, therefore, ideally be estimated simultaneously by a hydraulic model that can reflect wide area topography and geology. In this study, methods for estimating surface discharge after the construction of tunnels was proposed, and the capacity of conventional quasi three-dimensional groundwater flow analysis methods was enhanced so that calculation of groundwater inflow into caverns due to changes in groundwater level could also be made possible. The proposed method was applied to the granite bedrock around an actual reservoir, and it could accurately evaluate the groundwater and surface discharge conditions during rainfall over a wide area. Applicability of the method to the study of groundwater inflow in caverns and surface discharge was confirmed by numerical simulation.