Water flooding is widely applied for pressure maintenance or increasing the oil recovery of reservoirs. The heterogeneity and wettability of formation rocks strongly affect the oil recovery efficiency in carbonate reservoirs. During seawater injection in carbonate formations, the interactions between potential seawater ions and the carbonate rock at a high temperature can alter the wettability to a more water-wet condition. This paper studies the wettability of one of the Iranian carbonate reservoirs which has been under Persian Gulf seawater injection for more than 10 years. The wettability of the rock is determined by indirect contact angle measurement using Rise in Core technique. Further, the characterization of the rock surface is evaluated by molecular kinetic theory (MKT) modeling. The data obtained from experiments show that rocks are undergoing neutral wetting after the aging process. While the wettability of low permeable samples changes to be slightly water-wet, the wettability of the samples with higher permeability remains unchanged after soaking in seawater. Experimental data and MKT analysis indicate that wettability alteration of these carbonate rocks through prolonged seawater injection might be insignificant.