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This thesis is concerned with multiphase flow in porous media, focusing primarily on applications to oil recovery from subsurface rocks. The wettability of crude oil-brine-rock systems in petroleum reservoirs often exhibits mixed-wet states where effective contact angle varies locally, because surface active components such as asphaltenes in the crude oil can alter the wettability from its original water-wet to more oil-wet states. Furthermore, when a lower salinity brine than that of formation brine is injected to displace oil, which is known as low salinity water flooding, wettability alteration from a mixed-wet state to more water-wet condition can occur, resulting in an improvement of oil recovery. We use direct numerical simulation to study the impact of wettability and its alteration on multiphase flow in porous media at the pore-scale. A numerical model is constructed based on the lattice Boltzmann method with two newly developed numerical methods: a wetting boundary condition which precisely models contact angle, and a model to capture wettability alteration which changes contact angle depending on the computed local salinity. The numerical model is validated using several test cases where analytical solutions are available. In particular, the new wetting boundary condition is extensively validated using the static test cases of a flat, curved and staircase solid surfaces, and a dynamic test case of capillary rise. Water flooding in mixed-wet media is studied using the numerical model. Water flooding experiments imaged with a micro-CT by Alhammadi et al. are used in which hundreds of thousands of geometrically measured in situ contact angles are available using the method of AlRatrout et al. We show that a good agreement in both the fluid configurations and effective water permeability is obtained when we model the spatial distribution of contact angle on a pore-by-pore basis, but using higher contact angles than those measured in oil-wet regions of the pore space. This physically makes sense because the contact angle to use in simulations is the locally largest value that determines the threshold capillary pressure, whereas the geometrically measured angle may represent a hinging value on pores where displacement has not occurred. Using the matched simulation model to the water flooding experiments of Alhammadi et al., we study three enhanced oil recovery (EOR) methods -- low salinity water flooding, surfactant flooding, and polymer flooding -- through a parametric study changing fluid and/or rock properties of the simulation. This illustrates the use of a simulation model, namely to predict the behavior outside the range studied experimentally. We show the impact of these enhanced oil recovery methods on the microscopic displacement efficiency of the rock. Although this study does not consider the mixing between brine originally in the pore space and injected EOR fluids, this mixing is modeled for low salinity water flooding in the next study, using the two-phase lattice Boltzmann model coupled with mass transport of ions in water. We study wettability alteration caused by exposure to low salinity water using the new wettability alteration model. The numerical model is validated using two experiments performed at the pore-scale: detachment of oil droplets exposed to low salinity water by Mahani et al., and low salinity water flooding on a sinusoidal micro-model by Bartels et al. The phenomena observed in the experiments, including wettability alteration, detachment of oil droplets and recovery of trapped oil, are successfully simulated using a progressive wettability alteration driven by the slow development of thin water films implemented in the numerical model. The numerical model is, then, applied to micro-CT images of a Bentheimer sandstone. Higher oil recovery is observed in secondary mode injection compared to that of tertiary mode, whose mechanism is explained based on the simulation results, where a more stable displacement front is seen for secondary flooding. Lastly, we use the numerical model to validate recently developed pore-scale image analysis methods. A method to measure the interfacial curvature to obtain capillary pressure is studied. Through a comparison between measured curvature and curvature obtained from the simulated capillary pressure, the validation of the method and the assessment of its uncertainty is presented. We, then, validate a method to measure a thermodynamic contact angle by Blunt et al., through a comparison between the input contact angle of the simulations and the thermodynamic contact angle found from the simulated fluid configurations. Furthermore, we demonstrate how to use this method on a pore-by-pore basis to obtain the spatial distribution of wettability. We show that in mixed-wet media we can accurately capture the variation in local contact angle. Significant discrepancies are only seen in less consolidated media where the invading meniscus straddles several pores. Overall the thesis provides an improved method for direct simulation of flow in porous media which have undergone a wettability alteration. The work has been used to interpret experimental work and make predictions for local displacement efficiency for enhanced oil recovery processes. It has also been used to suggest methodologies to measure curvature and wettability from pore-scale imaging experiments.