Flow with free and rough surfaces near hydropower stations is of interest for both engineering and environmental applications. Here, Computational Fluid Dynamics simulations of free surface flow and flow over rough surfaces in regulated rivers were performed in applications such fish migration, spillway design and flow over rough surfaces as in hydropower tunnels or natural channels. For all the investigated applications it is typical with very large geometrical scales, high flow rates and highly turbulent flow. Modelling boundaries such as free water surfaces and rough walls presents a challenge and was given special attention as well as the treatment of turbulence. Validation of the numerical simulations was performed in all cases with me...