A finite difference model that simulates freshwater and saltwater flow separated by a sharp interface has been applied to estimate the salinity intrusion in the lower part of the Walawe River basin to the southern coastal aquifer, Sri Lanka. The effect of hydrogeological factors on the dynamics of the freshwater-saltwater interface has been considered through storage coefficients, porosity and hydraulic conductivity. The paper concludes that hydraulic conductivity is the main hydrogeological factor affecting the movement of the freshwater-saltwater interface, and the saltwater intrusion is more sensitive to groundwater recharge than hydrogeological properties. Therefore, the model was calibrated by adjusting the hydraulic conductivity to match the observed salinity profile in the southern coastal aquifer. Simulation results compare well with the observed long-term salinity profile suggesting that the numerical model can be used to successfully simulate the salinity profile in the area.