The development of Marine Renewable Energies leads to install structures in areas with strong and turbulent currents. In this kind of area, the vertical velocity profile is a function of the seabed roughness and of the tidal range, creating various velocity profile shapes. Bottom structures (tidal energy converter, sub-sea substation) are then brought to significant poorly understood wake and load variations. A generic study is thus developed to quantify the impact of vertical velocity profiles on a bottom-mounted obstacle in terms of load variations. This case study is also useful to better understand the energetic wake of a large obstacle in a tidal stream. Four velocity profiles are considered. Three are grid generated velocity profiles homogeneous transversely in the tank and one is the 3D flow generated by an isolated bottom cube. Loads on an aspect ratio cylinder of 6 and flow characteristics are analysed to characterise the impact that the different vertical velocity profiles can have on the behaviour of the cylinder in terms of load and wake evolution. The results show that an isolated roughness has a stronger impact on the bottom structure wake development than the vertical velocity profiles studied here, for which levels of the 1st and 2nd order statistics are slightly modified. The load analysis shows differences between each case, suggesting the strong impact of punctual large vortices.