Rice paddy water management was integrated into a distributed three-dimensional surface and subsurface coupling hydrological model of the Sakuragawa River watershed. This watershed is located in the Kanto Plain in Japan and includes the hillside of Mt. Tsukuba. Therefore, this watershed includes both steep mountainous areas and rice paddy-dominated flat land. Thus, water management of rice paddies is important and was calculated separately using a paddy model. The use of groundwater for rice paddy irrigation was considered as well as a water supply from outside of the watershed (Kasumigaura Lake). The model parameters were calibrated and validated with reference to the predictability of river water flow and the groundwater level. Using the calibrated model, three-dimensional streamlines, water travel time distributions, and water balance in some grids were clarified. The developed model will facilitate sustainable water resource management in the watershed.