Riparian vegetation does not only affect the channel flow carrying capacity, but also plays significant roles in water management, stream restoration, and river rehabilitation. This study numerically investigates the flow characteristics through longitudinally discontinuous rigid vegetation occupying half width of the channel, with the help of three-dimensional software FLUENT in which a Reynolds stress turbulence model was adopted. Three varying conditions of vegetation were considered comprising of vertically double-layered vegetation (DLV), submerged vegetation (SV), and emergent vegetation (EV) while keeping the same vegetation density, as well as a varying discharge condition against DLV was also tested. The results indicated that the flow distribution becomes more complex through DLV and SV followed by multiple layers with an inflectional instability in the vertical velocity profile around submerged canopy top, as compared to the flow through EV where the uniform distribution of flow over the canopy column was observed. The velocity in the canopy zone decreased considerably because of the resistance due to vegetation, which influenced the channel carrying capacity, in comparison to that in the non-vegetated zone. The flow velocities through the obstructed part of the channel, that is, canopy zone, in DLV arrangement reduced by a percentage difference of approximately 42 and 37% compared to that of SV and EV arrangements, respectively; whereas it was reduced by approximately 55% when the discharge was twice while keeping the same configuration of DLV. The inflectional instabilities and estimated mixing layer over the interfacial zone suggested a stronger lateral exchange of momentum for DLV configuration in comparison to that of SV and EV. Within the gaps between the patch zones, the flow velocity, turbulent kinetic energy, and turbulent intensity reduced significantly due to blockage effect and sheltering offered by the vegetation patches, signifying a positive flow response towards aquatic life and sediment deposition.