This paper presents a comprehensive three-dimensional Direct Numerical Simulation (DNS) investigation of flow characteristics over a roughened wall in a duct, exploring bulk Reynolds number variations from 4400 to 13,200 and considering the influence of side walls. Notably, a significant increase in friction factor highlights heightened resistance to flow due to surface roughness, emphasizing the importance of considering surface conditions in engineering applications. The study reveals three recirculation zones in the streamwise direction, indicating intricate separation phenomena caused by the interaction between the ribbed wall and the flow. Furthermore, the presence of sidewalls creates two major vortices perpendicular to the flow direction, highlighting the complexity of the vortical structures in this configuration, crucial for predicting flow behavior and optimizing system performance. The study demonstrates that the influence of the Reynolds number on these vortices is not well-scalable with respect to outer units, in contrast with respect to smooth ducts. Investigating side-wall effects, increased turbulent production rate, and non-equilibrium turbulence along the side walls highlight the sensitivity of turbulent stresses to Reynolds number and side-wall proximity. In conclusion, the paper provides novel insights into the interplay between Reynolds numbers, roughened surfaces, and boundary conditions in turbulent flows, laying a foundation for a deeper understanding of the flow in duct with high roughness.