The Motooka region in Fukuoka, Japan is a coastal region where agriculture is dominant. The green houses and wineries cover their water demand from groundwater. With the increased water demand, seawater intrusion is identified as an alarming threat to the Motooka coastal aquifer in near future. The measured electric conductivities of the water samples have been analyzed periodically. Until now the measured electric conductivities do not show high values but those values convince the emerging threat of seawater intrusion in this aquifer in future if groundwater will be pumped at current rate further. Therefore it is worth to conduct a numerical study of seawater intrusion and its impact to the Motooka area since the sustainability of the aquifer is inevitable for the future groundwater development and agriculture. In this paper a numerical study of the seawater intrusion of the Motooka is discussed. The numerical model presented in this paper was developed by coupling the groundwater flow equation with the mass transport equation to simulate the density dependent solute transport in the three dimensional space. The usage of this model as a management tool to simulate the salinity variation with groundwater pumping is emphasized. The numerical model was adequately capable of simulating the seawater intrusion and numerical results show a satisfactory agreement with the field observations.