Flow past wall-mounted cylindrical structures is commonly encountered in natural rivers where piers of bridge crossings or vegetation stalks are common within channels. In the current study, the influence of cylindrical structures on flow/bathymetric alterations for three different permeabilities is explored via two-dimensional numerical modeling. In model construction processes, the structure permeability is varied with the surface void ratio along the perimeter of the cylinder, i.e. the density of emergent and submerged solid elements is used to delineate the cylinder boundaries. The validation of this model is guaranteed through careful comparison with experimental data obtained for similar hydrodynamic conditions and cylinder properties. The validated model then is applied to investigate flow properties and scour and deposition patts with structure permeabilities of 0.0, 0.38, and 0.62. Simulated results show that a permeable structure has less impeding effects on flow than a solid cylinder. The wake ve-locity reduction decreases 38％ with a 63％ increase in the structure permeability due to increasing in-tensity of the bleeding flow through surface voids, causing less flow contraction and diversion, lower turbulent kinetic energy, and lower lee-side scour around the permeable structure and less deposition downstream under live-bed conditions.