In an era of water scarcity, accurate flow discharge measurement in open channels forms the cornerstone of hydraulic design and management. Portable sidewall-mounted semicircular (SMBF) flumes offer an ideal solution for laboratory and field applications due to their simplicity, portability, and high precision. However, the transition from free to submerged flow regimes complicates hydraulic performance, necessitating comprehensive investigation. This study employed a combined experimental and numerical approach to evaluate submergence effects on flow structures in SMBF flumes, using contraction ratios of 0.342 and 0.561 across diverse discharges (0.006 to 0.041 m³/s). Experiments were conducted at the Central Water Research Laboratory, University of Tehran, while numerical simulations utilized FLOW-3D software based on RANS equations and the RNG k-ε turbulence model, validated with R² = 0.95 and mean relative error below 8%. It was found that submergence reduced drawdown by up to 50%, lowers the Froude number from 1.2 to 0.8 (33% reduction), and decreases peak velocity by 40%, while extending the flow recovery length by 1 m. Turbulence intensity and vorticity were found to increase by approximately 100%, mean static pressure rises by 30%, and total head loss escalates from 0.1 to 0.3 (200%). These alterations diminish hydraulic efficiency but enhance flow stability. For precise discharge measurement, submergence ratios below 0.5 were recommended to minimize turbulence amplification and flow asymmetry. The findings yield improved calibration equations and provide a foundation for optimizing flume designs in irrigation and drainage networks.