This paper applies the Flow-3D to investigate the impacts of different flow discharge and vegetation scenarios on the flow velocity (including the longitudinal, transverse and vertical velocities). After the verification by using experimental measurements, a sensitivity analysis is conducted for the vegetation diameter, the vegetation height and the flow discharge. For the longitudinal velocity, the greatest impact on the flow structure originates from the vegetation diameter, rather than the discharge. The vegetation height, however, determines the inflection point of the vertical distribution. Comparing the transverse velocities at two positions in the vegetated area, i.e., the upstream and the downstream, a symmetric pattern is identified along the water depth. The same pattern is also observed for the vertical velocity regardless of the flow or vegetation scenario, including both transverse and vertical fluid circulation patterns in the vegetated area. Moreover, the larger the vegetation diameter is, the more evident these patterns become. The upper circulation occurs near the vegetation canopy. These findings regarding the circulations along the transverse and vertical directions in the vegetated region shed light on the 3-D flow structure through the submerged vegetation.