ABSTRACT Research on the vertical profiles of flow velocity in mountainous river channels is limited, particularly in scenarios where complex bed geometries are absent. Due to the coarse roughness and seepage flow on streambeds composed of gravel, the conventional formulae for flow velocity profiles derived from fluvial river channels do not apply to mountainous river channels. Based on flume experiments with a bed packed with natural gravel and a slope ranging from 0.006 to 0.16, we derived a theoretical formula for flow velocity profiles. This new formula integrates the influence of the subsurface flow and velocity reduction near the water surface, demonstrating a strong alignment with measurements. Our findings indicate that for shallow water flow over rough bed surfaces, the turbulence intensity diminishes along the vertical direction in the near-bed region while remaining relatively constant in the upper water body. Contrary to conventional theories which attribute the increase in flow resistance and the decrease in sediment transport rates in mountainous river channels to form drag, our study emphasizes that the subsurface flow plays a significant role in the overall flow resistance of mountainous river channels and should not be overlooked.