In this paper the application of a 3D numerical model covering the area of the Pentland Firth channel (Scotland, UK) to investigate the hydrodynamic and morphodynamic environment related to tidal energy extraction is presented in detail. The open source Delft3D flow model is used. Hydrodynamics of a regional Pentland Firth model provided the boundary conditions for a high resolution local scale model of the Inner Sound sub-channel, an area favoured for in-stream tidal turbines deployment. Investigation of the dynamics of substantial sandbanks located in this region during two spring-neap tidal cycles, under a ‘no-energy’ extraction scenario, showed that they are highly dynamic and their existence and integrity highly depends on the local flow regime. It is found that the observed tidal asymmetry along with the less significant secondary flows due to the curvature of the flow mainly contribute to the maintenance mechanisms of the sandbanks. Following that, the current model set up was used to investigate the impacts of tidal current turbines on sea bed dynamics. A range of energy extraction scenarios and array configurations was selected and modelled to map notable relationships between the altered currents and seabed changes.