In Kumamoto, Japan, about one million people depend for all their water on groundwater resources. Paddy fields and rice farming in the middle river watershed area make a large contribution to the groundwater recharge. In our research, an environmental measure (artificial flooding for groundwater recharge) conducted by local governments is evaluated. Hydrological measurement was conducted in a paddy plot in the area. A simple model of water distribution was developed on the basis of the field measurement. Then, drought risk in the paddy-field district was estimated using the model and GIS data. The results reveal that the fields with a high percolation rate of more than 30 mm/d result in inefficient use of irrigation water although they have large potential for groundwater recharge. In addition, the water distribution model suggests that environmental measures can increase the risk of water shortage in the paddy-field district due to the farmers' careless use of water.