A 3D numerical modelling study to investigate the existing hydrodynamic regime of the Pentland Firth Inner Sound Channel, Scotland, UK is presented. Hydrodynamics that govern some sensitive sedimentary deposits in the Inner Sound Channel are discussed. A 3D hydrodynamic model Delft3D is set up for Pentland Firth, located between Orkney Islands and mainland Scotland and a full sensitivity analysis of the numerical model is carried out. The current model set up sufficiently captures the existing hydrodynamics during a full spring-neap tidal cycle inside Pentland Firth. Using model results, the 3D structure of the dynamics of the tidal flows in the Inner Sound Channel is investigated. The temporal variability of tidal flows, the residual tidal flows in the channel and local flow interactions with the Island of Stroma are described. It is proved that the tidally dominant flows drive the sediment transport gradient model to explain the principle maintenance mechanisms of two island-associated sandbanks present in the Inner Sound. The present study provides detailed information on the physics of the tidal regime in the Inner Sound and explains the presence of sandbanks in an area of high tidal flows. Due to extremely high tidal flows, Inner Sound is considered as one of the most favourable sites for tidal energy extraction in the UK. The findings of this study will be very useful in assessing the significance of impacts of future tidal energy extraction on natural hydrodynamics and sediment dynamics of the area.