Granular bed protections are a common measure to mitigate scour of the sand bed around hydraulic structures. In view of marching towards cost-effective solutions to tackle erosion-related problems, it is important to accurately predict the loads exerted on the bed and come up with the needed rock grading. To that end, a 3-D eddy resolving modelling technique could help in formulation of a new stability formula, based on extreme local flow conditions It is the aim of this thesis to build a hydrodynamic numerical tool, able to predict governing mechanisms in stone stability. Special attention is paid on the way of representing a rough boundary and predicting wall and free turbulence. That being said, a Wall-Modelled Large Eddy Simulation (WMLES) is suggested and is build using the open-source CFD toolbox OpenFOAM. Firstly, simple open channel flow case simulations are set-up, to evaluate the performance of rough wall functions in the LES environment. Secondly, a backwards facing step kind of flow from the experimental study of Jongeling et. al (2003) is simulated and the performance of the numerical model is evaluated based on the experimental results. Finally, the suitability of this method for the target applications of this study is discussed, including a comparison with previous numerical studies of this research area.