River bathymetry is an important parameter for hydrodynamic modeling; however, it is associated with large bias because direct large-scale measurements are impractical. Recent studies adjusted river bathymetry data based on assessment of the difference between modeled and observed water surface elevation (WSE); however, river discharge model uncertainties can lead to unintended errors in the correction. In this study, we propose a simple but robust correction method using the WSE bias, based on stage–discharge rating curves rather than time series data. The rating curve represents only the characteristics of the river section, and is not sensitive to instantaneous errors. Our results showed that the “corrected river bathymetry” converged among discharge experiments driven by noise-corrupted runoff forcing. Given the difficulty of eliminating discharge errors, a method for correcting river bathymetry that is free from discharge errors is important for improving hydrodynamic modeling.