A simulation was done to analyze the seepage problems due to seawater intrusion through the embedded rock layers on heterogeneous layers of sea-dike. Numerical analysis with SAMTLE(developed by author) was done by taking various relative permeability $ratio(R_r/R_e)$. These results showed, when the sed-dike is newly designed, operated, and maintained considering the safety of sea-dike in seepage problems, these embankment materials are prudently chosen. The permeability of the soil materials, within the range of salinity management in freshwater, is comparatively high, however, the permeability of rock materials for bottom rock layer is low. Therefore, when the relative permeability $ratio(R_r/R_e)$ is bellow 10 it is safety in seepage problems of sea-dike.