Contaminant transport through soil liners with low hydraulic conductivity is both by advection and diffusion processes though the diffusion process is dominate. Diffusion coefficient of migrating species has to be considered to calculate the velocity of contaminant flume. Diffusion through a network of clay particles is slower and porous media diffusion coefficient (Dp) is used to consider tortuous flow paths around clay particles by tortuosity factor. Attenuation processes that occur further alter the diffusion coefficient while contaminants travel through the soils. Effective diffusion coefficient (De) takes into consideration of attenuation processes. It is known that the cation exchange capacity is an important factor for the attenuation of cationic species. While the normal cation exchange reactions that occur and consequent retardation of cations is well known, very little are known about the effect of anions on retention of cations. The effect of presence of sulphate ions on the effective diffusion coefficient of sodium, which is normally considered as conservative ion, in two different types of soils, has been studied. It has been shown that effective diffusion coefficient of sodium in the presence of sulphate are lower than values reported in literature due to exchange of sodium with calcium ions from the exchangeable complex of clay. Soil with higher cation exchange retains sodium better, making their migration much lower.