Utilization of recycled and reusable materials in construction industry has become an alternative way to substitute natural resources. However, national regulations might discourage to use them in construction works. With this understanding of the complexity, an alternative approach for utilization of naturally contaminated soils is proposed and numerically evaluated. The natural contaminated soil is deposited as a core material in the embankment with an earthen cover constructed from in-situ available soil. This research consists of two parts. At first, a water balance analysis was conducted using conventional equations for the cover layer. After that, a two-dimensional finite element contaminant transport analysis was performed with the advective-dispersive solute transport approach. Kyoto City, Japan, was selected as the investigation site, and its average monthly precipitation and mean temperature over the past thirty years were used as input data. Results reveal that annually approximately 28% of precipitation gets into cover from surface layer and the maximum percolation occurs on March. Moreover, it is concluded that the initial pressure head which is related to the initial saturation degree dramatically affects the contamination transport. Although the capillary barrier effects do not last for a long time, the contamination values will not be equal to source contamination within one-year period at the bottom of models. This is a promising finding for utilization of naturally contaminated soil in the embankments with a suitable design concept.