There are numerous springs around Suizenji and Lake Ezu area in the Kumamoto City which all of the tap water is sourced from groundwater. To estimate the groundwater discharge rate around Lake Ezu, the river flow rate at 13 sites in Kase River was observed monthly from December 1991 to December 2014. In previous studies, the total groundwater discharge rate was calculated as the difference in flow rates from lowermost-stream and uppermost-stream plus inflow rivers. In this study, the total groundwater discharge rate was calculated separately for Suizenji, Lake Kami-Ezu and Lake Shimo-Ezu zones. As a result, temporal variability of river flow rates was varied among sites and estimated groundwater discharge rate in each zone showed different variations. From 2003, monthly groundwater discharge rates were sometimes negative at the Shimo-Ezu zone. When the groundwater discharge rate in each separated zone is negative, calculations carried out with negative values (Case 1) and with positive values only (Case 2) are compared. As a result, total groundwater discharge gradually decreased from about 450,000 m³/day in 1992 to about 317,000 m³/day (Case 1) and 344,000 m³/day (Case 2) in June 2006. After the heavy rainfall in June and July 2006, the total groundwater discharge rapidly increased to about 430,000 m³/day in both cases. Temporal variability of total groundwater discharge was not so different between both cases, however, the minimum value in Case 2 was about 27,000 m³/day higher than that in Case 1 and the decreasing trend became moderate.