On December 26th 2004, a catastrophic tsunami devastated many countries of South East Asia. The inland saltwater surge impacted upon the coastal soil and groundwater quality in low lying areas. The groundwater resources along the coastal aquifers were affected through contamination and destruction to existing freshwater wells. Although most of the saline flood water eventually drained back to the sea and the period of flooding appeared short the sea water left a considerable salt load. For example, Pondicherry in India and Bande Aceh in Indonesia have both been severely impacted by salt contamination. These and many others around the world rely on groundwater for their domestic and agricultural needs. This paper investigates possible effects of a Tsunami type event on the Pine River’s coastal aquifer system. To simulate surface saltwater inundation a 3D density dependent flow and solute transport model was developed using finite element methods. The simulations show not only longer term influence on the aquifer water quality but also that a little change in soil water permeability could significantly alter the scenario.