Supercritical flows in mountain rivers create complex flow-obstacle interactions that govern infrastructure vulnerability and channel morphodynamics, yet current understanding remains focused mostly on smooth-bed assumptions that poorly represent natural gravel-bed channels, where grain-scale roughness fundamentally alters flow physics near the bed and around obstacles such as bridge piers and in-stream vegetation. This study quantifies how bed surface characteristics control velocity fields, turbulent structures, and bed stress patterns around obstacles in supercritical flow through high-resolution detached eddy simulations coupled with volume-of-fluid free surface tracking. We examined three morphodynamic states representative of natural channel evolution: smooth beds analogous to bedrock channels, rough flat beds representing post-flood recovery conditions, and equilibrium scoured beds representing quasi-steady morphodynamic states. Digital representation of detailed bed surface elevation, including individual sediment grains, was considered using Structure-from-Motion photogrammetry. Numerical simulations reproduced characteristic supercritical flow structures including wall-jet formations, horseshoe vortex systems, and reverse spillage phenomena across all bed configurations. We observed that grain-scale roughness completely transforms flow organization from coherent, predictable vortical structures to chaotic, grain-dominated flow fields. While smooth beds exhibit symmetric stress distributions with organized patterns, rough beds generate highly skewed distributions with extreme spatial variability, where coefficient of variation increases from 37 % to 115 %. Individual grains work as micro-obstacles, creating localized stress concentrations exceeding smooth-bed conditions by factors of 2–3, which can fundamentally alter sediment transport mechanisms. An equilibrium scour hole creates hierarchical flow disturbances where large-scale topographic modifications interact with grain-scale disruptions to produce the most complex stress fields observed. These findings demonstrate that engineering design standards based on smooth-bed assumptions can significantly underestimate the spatial heterogeneity and peak stress magnitudes characteristic of natural rough-bed conditions. The transition from organized stress patterns in smooth beds to grain-scale dominated physics in rough beds necessitates fundamentally different approaches to flow prediction, infrastructure design, and morphodynamic modelling in steep channel environments.