A numerical model was developed to evaluate the response of groundwater flow and the fresh-saltwater interface in relation to the construction of a particle accelerator at the coastal plain of Tokaimura, Japan. Undisturbed conditions were initially simulated and validated against field observations as a prerequisite for the analysis of predictive scenarios. Groundwater heads and the shape of the saltwater interface were appropriately described by the model, although it tended to underestimate salinity concentrations. Saltwater penetrated up to 250 m inland during predevelopment conditions, reaching more than 400 m at the dewatering phase. Flushing of entrapped saline groundwater might occur in addition to seawater intrusion. In depth, multiple saltwater fronts develop in response to the hydraulic properties of the sediments. Groundwater discharges offshore through the sandy aquifers, but salinity fronts prevail in the relatively impermeable layers. Routes for freshwater outflow turned into pathways of seawater intrusion during the pumping phase. The equilibrium would be reestablished within 2 years from the end of the stress, with no evidence of a permanent deterioration of neighbor residential wells. Nonetheless, after construction the accelerator forms a barrier that leads to a sharp rise in piezometric levels and creates a new and long-term disequilibrium in the saltwater wedge. Despite further work is still necessary to test many of the ideas proposed, the present study makes a new contribution to enhance the understanding of the processes occurring in coastal aquifers subjected to anthropogenic influence.