The grid-based water balance of watershed scale was assessed in the mountainous area of Pyosun catchment in Jeju Island after analyzing precipitation, evapotranspiration, and runoff from January 2008 to December 2013. The existing results of direct runoff, evapotranspirtion, and groundwater recharge comparing to precipitation were presented 22.0%, 25.6%, and 52.4%, respectively, in Pyosun catchment. However, this study indicated each component shows 14.5%, 24.2%, and 61.0%, respectively, in the mountainous area of Pyosun catchment. Therefore, groundwater recharge rate in the mountainous area appears higher than 10% comparing to the overall catchment. It would be analyzed that the amount of direct runoff is relatively small. Moreover, this difference could be generated because of the spatial discontinuities in the process of estimating the total amount of precipitation in the mountainous area. Therefore, the grid-based spatial analysis to maximize the spatial continuity would be useful for providing a more reasonable result when the total amount of water resources are evaluated in mountainous areas in the future.