River mega deltas are vulnerable to destructive flood risks due to their river flow characteristics. Despite this, it is still hard to model river flows in these regions. CaMa-Flood, a global hydrodynamic model overcame these limitations by using a bifurcation channel scheme that considers multiple downstream connectivities. Even with this scheme, uncertainties remain in modeling flows in non-primary channels, which are channels connected to the main stem of primary channels through bifurcation channels. In this study, the impacts of the bifurcation and non-primary channel depths to the river flow in Mekong Delta for CaMa-Flood are analyzed. Non-primary channels were treated differently from primary channels by imposing several channel depths for non-primary channels and bifurcation channels connected to them. There were seven simulations with depths from 0.05 m to 70.0 m. Small depth values (0.05 m to 0.25 m) bring worsening in the simulated flow values in non-primary channels. Large depth values (10.0 m to 70.0 m) bring improvements to simulated flow values in non-primary channel flow values in the delta as much as 25% for annual mean discharge and 46% for annual peak discharge. Moreover, there is an increase in the water received by non-primary channels based on annual mean discharge and peak flood depth. Overall, it was found that larger channel depths simulate flows in non-primary channels better. Uncertainties remain in the simulated flow. The next goal is to find more optimum river channel depths by starting from large depth values and finding a relationship between channel depths and other hydrological and geomorphological parameters that might be optimized to a global scale. Ultimately, the final goal is creating a bifurcation methodology that applies to global hydrodynamic models.