Study of turbulent flow over a rough bed is highly important due to its numerous applications in the areas of sediment transport and pollutant discharge in streams, rivers and channels. Over the past few decades, many experimental studies have been conducted in this respect to understand the underlying phenomenon. However, there is a scarcity in the number of computational studies conducted on this topic. Therefore, a Large Eddy Simulation (LES) of turbulent flow over a rough channel bed was conducted to contribute further understanding of the influence of bed roughness on turbulent flow properties. For this purpose, an efficient, second order accurate 'immersed boundary method' was implemented into the LES code Hydro3d-GT, and validated for flow past bluff bodies. LES results from the present study showed excellent agreement with previous experimental studies on flow over rough beds. An in-depth analysis of time varying turbulent quantities (like the velocity fluctuations) revealed the presence of coherent structures in the flow. Also, a three dimensional visualization of the turbulent structures provided a good picture of the flow, especially in the near bed region, which is quite difficult to accomplish using experimental studies.