In this paper, the application of a 3D numerical model covering the area of Pentland Firth channel (Scotland, UK) to investigate the hydrodynamics related to tidal energy extraction is presented in detail. A full validation analysis is carried out so that the fully operational 3D hydrodynamic model could be applied with confidence in order to explore possible impacts of tidal devices on the ambient marine environment. Following that, a higher resolution hydrodynamic and morphodynamic model covering the area of Inner Sound channel, between the Island of Stroma and Scottish Mainland, favoured for tidal energy extraction inside Pentland Firth, is set up. Preliminary results indicate that the existing morphodynamics of the observed sandbank areas inside Inner Sound Channel are very dynamic. In such a dynamic environment, results imply that possible alterations in tidal currents due to energy extraction may have some implications on the existing morphodynamic regime.