HYPOTHESIS: The change of wettability toward more water-wet by the injection of low salinity water can improve oil recovery from porous rocks, which is known as low salinity water flooding. To simulate this process at the pore-scale, we propose that the alteration in surface wettability mediated by thin water films which are below the resolution of simulation grid blocks has to be considered, as observed in experiments. This is modeled by a wettability alteration model based on rate-limited adsorption of ions onto the rock surface. SIMULATIONS: The wettability alteration model is developed and incorporated into a lattice Boltzmann simulator which solves both the Navier-Stokes equation for oil/water two-phase flow and the advection-diffusion equation for ion transport. The model is validated against two experiments in the literature, then applied to 3D micro-CT images of a rock. FINDINGS: Our model correctly simulated the experimental observations caused by the slow wettability alteration driven by the development of water films. In the simulations on the 3D rock pore structure, a distinct difference in the mixing of high and low salinity water is observed between secondary and tertiary low salinity flooding, resulting in different oil recoveries.