The paired catchments with the same basin size and meteorological condition but different geology were selected to compare the fresh submarine groundwater discharge (SGD) rate observed by seepage meters with value calculated from water balance method in Kumamoto, Japan. The fresh SGD rate decreases with the distance from the coast, on the other hands, recirculated saline SGD is higher at near shore due to wave set-up and at offshore due to tidal pumping. The spatial integrations of fresh SGD agree well with the water budget in both paired catchments. The difference of fresh component of SGD between two catchments may be caused by the difference of geology in the study area.