A model for simulating a long-term diffusion in concrete under submerged conditions has been developed. The model focuses on the interaction between cement hydrates and electrolyte solution adopting the physical properties of concrete as alternative parameters for estimating long-term diffusion. The model was verified by the large variety of long-term experimental data involving verification of cement hydrates, porosity properties, pH value, element distribution, and chloride penetration for sulphate-resistant Portland cement (SRPC) concretes. Evaluating impacts of hundreds of years' exposure on concrete durability, a simulation was also performed for an exposure time of 500 years. The results confirmed the importance of ion-cement-hydrate interaction in the evaluation of a long-term diffusion of harmful substances such as chlorides into concrete. The simulation results show also that the solid phases of the SRPC concrete mix that was used are stable in the long-term. The threshold concentration of chlorides which may initiate reinforcement corrosion defined as Cl-/OH- ratio could be exceeded in concrete after moderate exposure period under the conditions investigated with typical protective concrete layers. Using of case-specific values for a threshold chloride content and evaluating the method used for estimating the initiation time of reinforcement corrosion are recommended in the structures with a long-design service life.