The accurate simulation of moisture transport in cement-based materials is an important step to predict many durability processes of concrete structures. This paper studied the effects of boundary conditions on modeling moisture transport, in particular for simulating drying kinetics and the inverse determination of liquid water permeability. Three boundary conditions were investigated, namely, the Dirichlet (imposed) condition, the flux boundary condition, and the boundary supplied by moisture movement in the ambient environment (coupling with a convection-diffusion moisture transport model). By comparing with the measured drying mass loss curves (without airflow) for ordinary Portland cement pastes, we found that the Dirichlet boundary condition provides slightly better simulated drying kinetics than the flux boundary condition, while results of the coupling model are less promising. As for inversely determined liquid permeability, the studied boundary conditions lead to the max. 36% difference. If considering the airflow in the environment, both the flux boundary condition and the coupling model with computational fluid dynamics (CFD) show that the airflow does not have an effect on moisture evaporation for the studied cement-based materials, because of their low permeability, resulting in a very short initial stage of drying. Moisture evaporation for these materials is mainly controlled by the internal moisture transport. However, for materials with high permeability, the drying kinetics increase with the airflow velocity because the initial stage of drying becomes much longer than the low permeable materials. The implication is that some laboratory methods for drying cement-based materials (specimens stored in a sealed chamber without airflow) may need to be reevaluated because the relative humidity at the material surface is different from the controlled relative humidity.