This study evaluates the use of two Computational Fluid Dynamics (CFD) techniques in calculating the three-dimensional flow and bed shear stress distribution in a regulated river reach near Trondheim, Norway. The two different CFD codes being used in this study are: one commercial FLOW-3D and an in-house program, SSIIM, developed by the third author (NRBO). One of the primary differences between the programs is that FLOW-3D uses an orthogonal, structured grid, while SSIIM uses a non-orthogonal unstructured grid. Flow-3D computes the location of the free water surface based on a volume of fluid method. In the current study, the water surface profile was computed using a 1D backwater computation with SSIIM. Both programs use first- or second-order schemes for the convective term in the Navier–Stokes equations, and the study investigated both options for the two different models. The computed results were compared to ADCP measurements obtained from three cross sections of the river. The comparison showed a good agreement between calculated and measured velocities when using higher-order discretization schemes. Using a first-order upwind scheme, the results deteriorated somewhat due to false diffusion. The results of this current study could be beneficial for the estimation of fluvial erosion, which causes severe damages to riverine areas.