Abstract In this paper the development of a quasi-three-dimensional numerical model that can be used for quantifying groundwater inputs and associated contaminant discharged from coastal aquifers into the coastal zone at a regional scale is presented. The present model is called MODSharp. In order to handle problems at a regional scale, the sharp interface approach which is used for conceptualising seawater intrusion, is applied to this model. This model can be used for the simulation of groundwater flow and contaminant transport in layered coastal aquifers at a regional scale. The method of characteristics is used to solve the advection-dispersion equation, which governs contaminant transport in coastal aquifers. In this study, MODSharp is used to investigate the influence of Sea Water Intrusion Interface (SWII) on the temporal and spatial variations of contaminant flux from coastal aquifers into the sea. Thus, a large number of simulations for different scenarios are performed. For the case that the land-ward boundary condition is constant head, it is shown that simplification and neglecting the effects of SWII causes an erroneous estimate of the speed of the contaminant plume movement towards sea. The value of hydraulic conductivity is shown to have a significant effect on the amount of discharged contaminant. Finally, it is concluded that over-simplification of the sea-ward boundary condition in numerical simulations, causes an incorrect estimate of temporal and spatial variations of the discharged contaminant into coastal water.