The simulation of the contaminant transport to determine the penetration of sea-water front is extremely complex due to the uncertainty related to the depth and orientation of the fault network and also due to the diffusion phenomenon associated with the variable density between fresh and salt water. Furthermore, the pumping activity which takes place in the aquifer is variable upon demand and affects significantly the hydraulic characteristics of the aquifer during the simulation period. In this paper, using the FEFLOW numerical simulator a subsurface flow and contaminant transport model that estimates the penetration of seawater intrusion front for a karstified coastal aquifer in Crete, Greece was developed. The model takes into consideration the geomorphologic characteristics of the karstic system and the density-dependent groundwater flow. The model results showed that the connectivity of the fractures and the fluid density effects are important factors that drive the seawater intrusion front asymmetrically inland.