Seawater intrusion is considered as one of the main processes that degrade water quality by raising salinity to levels exceeding acceptable drinking water standards. Over-abstraction is the main cause of seawater intrusion. Moreover, climate change and sea level rise speed up seawater intrusion. This paper presents the development of a coupled transient finite element model for simulation of fluid flow and solute transport in soils and its application to study seawater intrusion in Gaza aquifer. The effects of likely sea level rise due to climate change and over-pumping on seawater intrusion in Gaza aquifer are studied using three scenarios: rise in sea level due to climate change; decrease in piezometric head on the land side due to over-pumping; and a combination of sea level rise and over-pumping. The results show that a rise of 1 m in sea level has a significant effect on the position of the transition zone and can result in a further 0.5 km seawater intrusion in Gaza aquifer. However, the combination of sea level rise and over-pumping results in movement of the transition zone further inland (nearly 1.0 km). The results show that Gaza aquifer is subjected to severe seawater intrusion from the Mediterranean Sea and there is an urgent need to protect the aquifer from seawater intrusion.