Flows at tidal-stream energy sites are characterised by high turbulence intensities and by the occurrence of highly energetic large and coherent flow structures. The interaction of the flow with seabed roughness is suspected to play a major role in the generation of such coherent flow structures. The problem is introduced with canonical wall-mounted square obstacles representing abrupt changes of bathymetry, with high Reynolds number flow (Re = 250000). Two methods are used: a numerical model, based on the LBM (Lattice Boltzmann Method) combined with LES (Large Eddy Simulation) and an experimental set-up in a circulating tank. The numerical model is validated by comparison with experimental data. In the case of a wall-mounted square cylinder, large-scale turbulent structures are identified in experiments where boils at the free surface can be observed. LBM simulation allows their three-dimensional characterisation. The dynamic of such large-scale events is investigated by temporal, spatial and spectral numerical analysis. Results show that periodical Kelvin–Helmholtz vortices are emitted in the cylinder wake. Then, they merge to form larger and more coherent structures that rise up to the surface. A wavelet study shows that the emission frequency of the Kelvin–Helmholtz vortices is not constant over time.