A generic computational model describing the evolution in the 3D space and time of the fresh and salt water movement (two layers 2DH) and the intrusion of salt water in coastal aquifers is formulated and solved. The model has been validated and compared with analytical solutions produced by Strack and with experimental results, for specific flow conditions, produced in the flume of the Hydraulics laboratory of Thessaloniki TEI. A sensitivity analysis to the model parameters is conducted. Two interesting tests refer to the issue of increased seawater intrusion due to the forecasted sea level rise for almost 1m during the 21st century and due to the negative trend of precipitation on the Mediterranean coast. Two alternative methods to increase the aquifer’s sustainable productivity by artificial means are preliminarily tested, namely: a) use of recharge canals and b) use of distributed scavenger wells placed between the productive wells and the coastline.