Climate change might lead to sea level rise, changes in the frequency, intensity and duration of wave storms, which will lead to an increase of coastal flooding events. One of the most important long-term effects of coastal floods is saltwater intrusion induced by the vertical infiltration of the salt water behind the overtopped and/or breached coastal barriers. A single overflow event may contaminate the freshwater aquifer for several years until it is remediated naturally under the effect of precipitation and subsequent seaward directed flow. The main objective of this study is to understand the effects of a maritime storm and the induced hinterland inundation on the water quality of a coastal aquifer. The study targets the municipality of Almada (Portugal) which has an extensive coastline, with coastal aquifers with high susceptibility to contamination, namely the unconfined aquifer of the coastal plain of Costa da Caparica. Groundwater flow modelling and mass transport in the aquifer were modelled using the MODFLOW and MT3DMS software. The aquifer contamination by an overflow was modelled considering wave overtopping and flooded area on the coast was estimated from previous works that coupled a wave transformation model (SWAN) with a high-resolution swash model (XBEACH). The extent of the subsurface contamination is a function of the flood extent. Results showed that at an extreme storm event, waves can overtop the coastal dune causing a coastal flood that extends approximately 160 meters inland with a significant increase in chlorine concentration in the aquifer. Recover of the aquifer to previous concentrations was found to take several years.