To understand the underlying phenomena that drive concrete deterioration under cyclic environmental conditions in the marine environment, a reactive transport model (RTM) for unsaturated cement-based materials has been established in this study, including multi-ionic and moisture transport coupled with a chemical equilibrium computation. The two-phase moisture transport model, which considers pore structure changes, is introduced with capillary pressure as the primary variable parameter. The modified Poisson-Nernst-Planck (PNP) equations were illustrated for multi-ionic transport through pore solution under unsaturated conditions. A modelling approach for moisture conductivity based on the pore structure and moisture storage was presented to account for pore structure changes on the mass transports. The consideration of boundary conditions and moisture flux through the exposed surface is demonstrated for wetting and drying conditions, separately. Numerical results for mortar samples subjected to NaCl solutions under various cyclic wetting and drying conditions were in good agreement with experimentally measured moisture gain and total chloride content. Under more prolonged wetting conditions, the deeper influence depth and a wider range of moisture fluctuation lead to an increase in concrete deterioration. For all cyclic wetting conditions, the precipitation of Friedel's salt is predicted, which subsequently limits the transport of chloride ions to deeper depths from the exposed surface. A peak in the chloride profile is observed near the exposed surface. Meanwhile, the peak region continuously expands and moves deeper into the specimens with increasing wetting time duration and exposure times, consistent with Friedel's salt precipitation. In contrast, the chloride content near the exposure surface shows a significant decrease due to the decomposition of the C–S–H phase caused by ion leaching and carbonation of the exposed surface.