To estimate the spatial distribution of groundwater discharge from the bottom of a small lake of Kumamoto in Japan, we applied continuous radon measurements with a dual loop system and verified the results obtained using the radon method by visual diving surveys. Time-shifting correction in the dual-loop system is reasonable to obtain the true radon activity in water. Distributions of radon activity and water temperature in the study area reveal the effects on groundwater discharge and mixing situation of lake water. The estimated discharge zone ascertained using the radon method agrees with the groundwater discharge distribution observed through diving surveys. Although the data resolution of the radon method is much greater than the width of observed discharge zones, the general distribution of groundwater discharge is recognizable. The dual loop system of radon measurement is useful for smaller areas.