The main objectives of this study is to model the transport of methylene blue (MB) in homogenous and layered soils which has been studied experimentally by fixed bed column. The effect of soil stratification has been studied through numerical investigation based on the coupled solute transport model in three-layered soil. The effect of some significant parameters such as flow rate, initial concentration of MB, thickness of each layer and the numbers of layers on the breakthrough curves have been undertaken. A finite element analysis model was employed to predict the transport of MB in soils. A two dimensional model based on Richards equation and advection-dispersion equation coupled with adsorption model has been developed and an analytical model has been used to predict the dispersivity. The results shows that the soil heterogeneity has a significant effect on methylene blue (MB) adsorption through unsaturated layered media and the effect of the parameters of the upper layer of the soil is more significant than those of the lower layer but this effect can be controlled with the choice of the thicknesses of each layer.