New chloride diffusion coefficient is proposed in order to estimate the effect of chloride binding and evaporable water on chloride ion penetration in marine concrete structure. A finite element method program developed on the basis of the new diffusion coefficient provides an estimation of chloride concentration according to concrete depth, external and internal conditions, and the predicted chloride concentrations are compared with experimental values. The new diffusion coefficient, which is presented as functions of chloride binding, evaporable water and intrinsic diffusion coefficient, varies greatly according to water-cement ratio. But, curing temperature does not have a significant influence on the ratio of modified diffusion coefficient to intrinsic diffusion coefficient. The FEM program using the modified diffusion coefficient estimates experimental chloride concentrations in a little error range. The numerical analysis for internal and external conditions proposes that the most effective way to reduce chloride ion penetration is to decrease water-cement ratio.