Tidal turbines at sea are subject to complex flow conditions. Among that complexity, wide bathymetry obstacles can generate powerful coherent flow structures whose impact on horizontal axis tidal turbines was proved to be highly detrimental. Consequently, the present paper aims at studying the effects of such coherent flow structures on the response of another tidal turbine geometry, namely a bottom-mounted ducted twin vertical axis tidal turbine (2-VATT). We tested a 1/20 scale model of such a 2-VATT in Ifremer’s flume tank either with a flat bed or downstream of a wide bathymetry obstacle at a constant far upstream velocity and we measured the turbine response simultaneously with the flow velocity. These flow measurements make it possible to compute cross-correlations in order to analyse the influence of the velocity fluctuation on the turbine response. The results reveal a strong drop in the average power and loads coefficients of the 2-VATT combined with significantly larger fluctuation. The velocity deficit and the high level of turbulence in the obstacle wake is responsible for a 40 % lower average power coefficient and more than 3 times higher standard deviation compared to the flat bed configuration. The loads standard deviations are multiplied by 2 for the drag and by 10 for the lift when the 2-VATT is downstream of the bathymetry obstacle. This behaviour strongly increases the risks of structural fatigue failure, but the turbine drifting or overturning risks under those conditions remain lower than with the flat bed. The power fluctuation increase appears to be mostly due to the flow shear in the obstacle wake whereas the load fluctuation is mostly due to the periodical passing of the coherent flow structures. Thus, a proper characterisation of the flow at each precise turbine locations prior deployment at sea is highly recommended to design their structure accordingly.