Due to the presence of a monopile in a turbulent flow swirling vortices, known as horseshoe vortices, can form upstream of the structure near the cylinder-bed junction. Those vortices then travel downstream of the cylinder as they are being dragged along with the current. The horseshoe vortices can scoop up bed material surrounding the cylinder, weakening the foundation of the structure. This phenomenon is known as scour. A common protection method to reduce the effects of scour is the dumping of stones in the vicinity of the cylinder-bed junction. The aim is to alter the flow dynamics near the bed in such a way that the underlying sediment is mostly unaffected. However, the protection material itself is also subject to hydrodynamic forcing and can therefore be entrained as well. This would be described as damage to the protection layer as its effectiveness reduces due to re-exposure of the underlying sediment. It is for this reason that protection layers must be carefully designed depending on their use. The mechanism of the horseshoe vortex system and its damaging aspects are not completely understood yet, making engineering of specific protection layers challenging. To better understand the flow behaviour upstream of a cylinder-bed junction, where the formation of the horseshoe vortices takes place, several tests have been performed at the Eastern Scheldt Flume in the Hydro Hall of Deltares. Here different cylinder and bed protection configurations were subjected to turbulent current and wave conditions where the upstream flow fields were measured with a PIV measurement system. Since the obtained information of the tests is limited to a specific area, there was an interest in modelling the test cases by means CFD, while using the test results as validation. In this thesis several of the test cases have been modelled with the Improved Delayed Detached Eddy Simulation (IDDES) hybrid turbulence model, based on the Spalart-Allmaras formulation, which include the following: a) Open channel with a smooth bed and no monopile b) Open channel with a rough bed and no monopile c) Open channel with a smooth bed and a smooth monopile d) Open channel with a rough bed and a smooth monopile The modelling strategy used starts off with a basic simulation case (a) which is compared to the test results for validation of the simulated flow characteristics. This model is then elaborated on by inclusion of either a rough protection model (b) or a smooth cylinder (c). Both models are again validated with the test results so that the ability of the IDDES model to model the fluid-structure interaction is investigated. Finally, a simulation that includes both a rough bed and a smooth cylinder (d) is performed. For simulation models b, c and d an assessment is made for potential initial particle entrainment by means of hydrodynamic forcing indicators. Additionally, the effects of bed model surface roughness on the entrainment of bed material are briefly considered.