The depth of low permeable layer in Jeju Island was analyzed using the geologic columnar section data. The highest low permeable layer was found in center of Mt. Halla and the deepest area was in eastern part of Jeju Island. The study area, Seongsan watershed, is located in the eastern part of Jeju where the low permeable layer showing deep in a northward direction. Based on this analysis, the MODFLOW modeling was performed for groundwater flow of Seongsan watershed. The boundary of Seongsan watershed was set up as a no-flow and the modeling result showed the difference -0.26~0.62 m compared to the observed groundwater level. Meanwhile, MODFLOW model results considering low permeable layer showed -0.26~0.36 m differences compared to groundwater level and indicated more accurate than no-flow method result. Therefore, to interpret the groundwater flow over Seongsan watershed, comprehensive consideration including the low permeable layer distribution below the basalt layer is needed.