The effects of fractures in rock masses on the groundwater flow and the groundwater flow system in the volcanic rocks are analyzed by GFFP-WT model, which allows more realistic analysis of groundwater system by considering the fractures in rock masses. The evaluation of the effects of fractures in rock masses on the groundwater flow has been carried out in the 2nd Yeonwha and resulted in that the fractures mostly influence flow time because of hydraulic head distribution change. The results of the groundwater flow system analysis in the volcanic rocks are as follows. Most of groundwater once flowed in Lapilli tuff flowed out through Lappilli tuff layer. But only a small fraction of water flowed out through crystal tuff layer.