AbstractAccurate estimation of mean flow velocity is crucial for hydraulics and soil erosion studies. A correction factor (α) is required to convert flow surface velocity to mean velocity when using the dye tracer method. However, the determination of an appropriate α value is challenging and little information is available about how α varies with progressive inundation conditions, especially for rough surfaces with protruding roughness elements (e.g., stones). Therefore, laboratory experiments were conducted in a flume with sandpaper (SD) and stones (ST) surfaces to investigate the impact of roughness elements on the correction factor with varying inundation conditions. The results showed that using a single α value is inappropriate for rough surfaces. The correction factor was positively correlated with the Reynolds number and is controlled by flow regimes as well. Moreover, the impacts of inundation conditions as well as protruding roughness elements should be taken into account for determining α. Correction factor varied non‐monotonically with inundation ratio, depending on the progressive inundation status of protruding roughness elements. The developed equations introducing the inundation ratio performed well in predicting α, with R2 = 0.86 and NSE = 0.91. The results contribute to our understanding of measuring mean flow velocity using the dye tracer method.