This study adopted the Modflow, a three-dimensional groundwater model, to proceed the groundwater level fluctuation in the Shueishe dam of SunMoon Lake during the period of Typhoon Morakot. The rainfall records show that cumulative rainfall depth reach 777 mm, which induces the fast rise of groundwater level in three wells located in the downstream of longitudinal direction of dam. Using the Modflow software and the trial-and-error method, the groundwater level distributions and the hydraulic conductivities in the downstream of dam were resolved. However, due to the lack of the groundwater well in the lateral direction of dam, we cannot be informed of the discharge of groundwater from the flank of dam. Therefore, the groundwater wells should be also installed in the longitudinal and the lateral direction, so as to obtain the flow direction of groundwater.