Proper estimation of contaminant transport rate through compacted fine-grained soils assumes great importance in the context of remediation of contaminated sites. Integrated use of equilibrium and mass transfer rate tests in conjunction with appropriate mass transfer models provide a useful framework for evaluating leaching of contaminants such as lead (Pb2+) and zinc (Zn2+), which have relatively low pH-dependent solubility. In this article, column experiments were set up to study the diffusion coefficients and break through times using method of slices for two semi-arid soils (Al-Ghat and Al-Qatif) for selected heavy metals (Pb2+ and Zn2+). The studies were carried out on soil samples before and after amending with lime. Breakthrough curves were obtained under different hydraulic gradients for the compacted mixtures and the diffusion coefficients for Pb2+ and Zn2+ were evaluated using POLLUTEv7 relying on advection-dispersion equation, for a liner thickness of 1m. The current study allowed us to observe the movement of contaminants in the clay liners to be predicted in real time. Break through curves showed relatively higher retention levels for the targeted metal ions. The retention strength of these soils was observed to be constant up to five pore volumes, corresponding to the pH of the effluent and pore water of soil slices. Soils amended with lime showed an improvement to the order of 10 times in retention capacity. Under pure diffusion controlled migration both soil lime mixtures performed very well and gave breakthrough times of more than 400 years whereas advective-diffusion gave break through times of 200 years for both metal ions considered in the study.