Groundwater discharge to sea areas affects environmental conditions along coasts. Enclosed bays may experience eutrophication caused by nutrient input from land areas through groundwater discharge since groundwater is often contaminated by large amounts of nutrients as compared with river water. Therefore, it is necessary to estimate the groundwater discharge into seas quantitatively in order to understand nutrient pathways. A distributed groundwater recharge model was developed in order to estimate total groundwater discharge flow into the Ariake Bay, in Kyushu, Japan. The Komoda catchment within the Kikuchi River basin in Kumamoto prefecture was studied as a representative area for the Ariake Bay. The model partitions rainfall into direct runoff, evapotranspiration, and groundwater recharge. Parameters are set based on land use. Groundwater discharge is calculated using a water balance approach. The results show that groundwater discharge into the Ariake Bay from Kukuchi River basin is on average 123 mm year-1. The groundwater discharge accounts for about 8% of total water discharge and 9% of river discharge. The results can be used to better estimate annual transport of nutrients in the groundwater to the sea and thus also to better manage eutrophication problems.