We developed a pore-scale reactive multicomponent twophase flow and transport numerical model to study the pore-level dynamics of water injection in carbonate rocks. The model utilizes direct numerical simulation of Navier−Stokes equations and a newly tuned surface complexation model (SCM) for brine−calcite interactions. An SEM image of chalk mimicking the heterogeneous pore network of the rock is initially saturated with oil and brine and then flooded with brine. With the SCM, we calculate the ζ-potential at the calcite surface under different chemical conditions. The change in the ζ-potential triggered by the shift in the chemical conditions is then related to the variation in the contact angle. We then used the developed coupled model to explore the impact of varying brine compositions, injection sequences, matrix connectivity, and injection rates on the pore-filling sequence and sweep efficiency. Our results demonstrate how the changes in the contact angle, injection rate, and pore connectivity control the displacement process and the ultimate recovery. Injection of modified salinity water results in a later breakthrough time than formation waterflooding. Further, our results confirm that the tertiary mode injection of modified salinity brine is less effective than the secondary mode of modified salinity brine flooding.