To clarify the mechanism of water transport in mortar, a three-phase model consisting of fine aggregate-interfacial transition zone (ITZ) -cement paste was developed to represent mortar, and then the water transport process in mortar was simulated by a partial bounce-back lattice Boltzmann method (PBB-LBM). The influences of aggregate volume fraction, the ITZ’s thickness and pore structure on the water permeability of mortar were evaluated. The results show that mortar’s water permeability declines at an increased aggregate content and it is always below cement paste’s water permeability at a thin thickness of ITZ and a low porosity. Once the thickness of ITZ exceeds 150 μm or its effective porosity is two times greater than that of cement paste, the permeability of mortar is close to or even above the matrix’s water permeability. This is attributed to the competitions among the ITZ effect, aggregate dilution effect and tortuous transport path in mortar.