The contaminant transport mechanism in fractured clay porous media has been analysed using numerical modelling. Implicit finite difference has been used to develop the numerical model. A constant continuous source of contaminants has been assumed at the inlet of the fracture. The domain is considered to be saturated. A varying grid is considered in the fracture skin to account for the flux transfer at the interface of the fracture and the skin. The effect of constant dispersion as well as distance-dependent dispersion on the contaminant transport mechanism has been analysed in the presence of fracture skin. The contaminants are assumed to follow Freundlich non-linear sorption isotherm. Sensitivity analysis has been conducted to study the effect of different fracture-skin porosities, skin diffusion coefficients, half fracture apertures, fluid velocities and skin thicknesses on the solute transport mechanism within the fractured clay porous media. Results suggest that amount of solute diffusion into the clay matrix is directly proportional to the fracture-skin porosity and fracture-skin diffusion coefficient and inversely proportional to thickness of the half fracture aperture and the fluid velocity. The role of non-linear sorption is insignificant and scale-dependent dispersivity results in enhanced mass diffusion from the fracture. © 2014 Indian Society for Hydraulics.