A new method to study 3D saline front advancement in coastal fractured aquifers has been presented. Field groundwater salinity was measured in boreholes of the Bari (Southern Italy) coastal aquifer with depth below water table. Then, the Ghyben-Herzberg freshwater/saltwater (50%) sharp interface and saline front position were determined by model simulations of the freshwater flow in groundwater. Afterward, the best-fit procedure between groundwater salinity measurements, at assigned water depth of 1.0 m in boreholes, and distances of each borehole from the modelled freshwater/saltwater saline front was used to convert each position (x, y) in groundwater to the water salinity concentration at depth of 1.0 m. Moreover, a second best-fit procedure was applied to the salinity measurements in boreholes with depth z. These results provided a grid file (x, y, z, salinity) suitable for plotting the actual Bari aquifer salinity by 3D maps. Subsequently, in order to assess effects of pumping on the saltwater-freshwater transition zone in the coastal aquifer, the Navier-Stokes (N-S) equations were applied to study transient density-driven flow and salt mass transport into freshwater of a single fracture. The rate of seawater/freshwater interface advancement given by the N-S solution was used to define the progression of saline front in Bari groundwater, starting from the actual salinity 3D map. The impact of pumping of 335 L·s−1 during the transition period of 112.8 days was easily highlighted on 3D salinity maps of Bari aquifer.