A large-eddy simulation (LES) of a laboratory-scale horizontal axis tidal stream turbine operating over an irregular bathymetry in the form of dunes is performed. The Reynolds number based on the approach velocity and the chord length of the turbine blades is approximately 60,000. The simulated turbine is a 1:30 scale model of a full-scale prototype and both turbines operate at very similar tip-speed ratio of λ ≈ 3. The simulations provide quantitative evidence of the effect of seabed-induced turbulence on the instantaneous performance and structural loadings of the turbine revealing how large-scale, energetic turbulence structures affect turbine performance and bending moments of the rotor blades. The data analysis shows that wake recovery is notably enhanced in comparison to the same turbine operating above a flat-bed and this is due to the higher turbulence levels generated by the dune. The results demonstrate the need for studying in detail the flow and turbulence characteristics at potential tidal turbine deployment sites and to incorporate observed large-scale velocity and pressure fluctuations into the structural design of the turbines.