Seawater injection is widely used to maintain offshore-oil-reservoir pressure and improve oil recovery. However, injecting seawater into reservoirs can cause many issues, such as reservoir souring and scaling, which are strongly related to the seawater-breakthrough percentage. Accurately calculating the seawater-breakthrough percentage is important for estimating the severity of those problems and further developing effective strategies to mitigate those issues. The validation of using natural-ion boron as a tracer to calculate seawater-breakthrough percentage was investigated. Boron can interact with clays, which can influence the accuracy in seawater-breakthrough calculation. Therefore, the interaction between boron and different clays at various conditions was first studied, and the Freundlich adsorption equation was used to describe the boron-adsorption isotherms. Then, the boron-adsorption isotherms were coupled into the reservoir simulator to investigate the boron transport in porous media, and the results in turn were further analyzed to calculate the accurate seawater-breakthrough percentage. Results indicated that boron adsorption by different clays varied. pH value of solution can significantly influence the amount of boron adsorbed. As a result, the boron-concentration profile was delayed in coreflood tests. The accuracy of the new model was verified by convergence rate tests and comparison with analytical results. Furthermore, model results fit well with experimental data. On the basis of the reservoir-simulation results, the boron-concentration profile in produced water can be used to calculate the seawater-breakthrough percentage by considering the clay-content distribution. However, the seawater-breakthrough point cannot be determined by boron because the boron concentration is still at the formation level after seawater breakthrough due to boron desorption.