<p>Wind tunnel experiments using Particle Image Velocimetry method were conducted to compare the flow characteristics induced by slender square and circular cylinders fully immersed in the boundary layer at gap ratios from 0 to 2. The results indicate that the shedding vortex is suppressed by the presence of the bottom wall in both flows if the wall-cylinder gap distance is lower than a threshold. However, the threshold gap for the square cylinder is lower than that for the circular cylinder. Although the scales of the large-scale turbulent structures are significantly reduced by the presence of cylinder, the two types of disturbed boundary layer have a similar downstream recovery process, without significant scale difference due to the small characteristic size of the disturbing cylinder. Since the near-wake flow behind the square cylinder is larger than that behind the circular cylinder for the same gap, the shedding vortex exhibits noticeably different contributions to the energy fraction of various turbulent modes. For boundary layer disturbed by the square cylinder, the Kármán vortex street becomes the dominant structure in the third and fourth order modes, whereas the effects are visible in the 4-10th order turbulent modes in the circular-cylinder disturbed boundary layer if the gap is high enough.</p>