Management of groundwater resources involves the allocation of groundwater supplies and water quality to competing water demands and uses. The resource allocation problem is characterized by conflicting objectives and complex hydrologic and environmental constraints, especially in coastal aquifers. The development of mathematical simulation models provides groundwater planners with quantitative techniques for analyzing alternatives groundwater resources management. The gathered knowledge was then used to build and to calibrate a 3D transient model of 45 years time period (1963-2008). The numerical model was used further to discuss some issues on the management of the regional groundwater resources. The calibration of the 3D model has been achieved in a time dependent, iterative and semiautomatic fashion. This paper describes a 3-D seawater intrusion modeling process for a specified study area in Eastern Coast aquifer, in NE Tunisia. The simulation results presented in this paper are based on the density-dependent miscible flow and transport modeling approach for simulation of seawater intrusion in coastal aquifers. Response evaluations consider the effects of vertical recharge on seawater intrusion, effects of boundary conditions, and effects of spatially varying pumping from the aquifer.