Turbulent flow over a permeable layer is found in many natural systems such as gravel bed streams, as well as in many artificial structures. For this kind of flow, the flow domain consists of a free stream zone and a porous zone each zone have distinctly different flow features. The interface between these two flow zones is much less understood than both free stream and porous media flows. Further investigations are required in order to improve understanding of mass and momentum exchange processes, which take place within the interface zone, where free surface flow and porous media flow affect and alter each other. This thesis presents a computational fluid dynamic (CFD) investigation of turbulent flow and a tracer migration in a system, consists of a free surface and a permeable layer. Five cases, covering a range of flow depths and porosities of permeable layer, were analysed. The detailed two-dimensional flow simulations were carried out and were validated using the experimental results of Prinos et al. (2003). The results of simulations were up-scaled by spatial averaging over the free stream zone and the porous zone. In this project, the penetration depth associated with momentum and mass penetration. The results show that increasing either the water depth or porosity of the porous layer increases the both roughness mass penetration thicknesses. Several models were applied (i) a one-box model containing advection and the dispersion in the free-surface; (ii) a two-box model containing the advection and the dispersion in both the free-surface and the porous zone. (iii) a three-box model with the interface zone in between the free stream and the porous zone. The parameters for all these models were evaluated and then cross-compared. The three-box conceptual model is novel, and it represents the main contribution from this thesis.