Abstract: Model uncertainty has always been considered as an important issue in the study of mathematical models. In this study, a physical model of the upper Toce River section of 5 km long is used to investigate the uncertainty in two-dimensional hydrodynamic model parameters, boundary conditions, and their interaction, by using the Latin hypercube sampling-generalized likelihood uncertainty estimation (LHS-GLUE) and the shuffled complex evolution metropolis-UA (SCEM-UA) methods. Sensitivities of model parameters and boundary conditions to water level are analyzed using partial rank correlation analysis. The results indicate that the sensitivity of Manning’s roughness coefficient of the hydrodynamic model to water level is greater than that of the boundary conditions and it has spatial-temporal variability. Either of these two methods could give a reasonable uncertainty interval in water level simulations, but compared with GLUE, SCEM-UA could better estimate the posterior distribution of model parameters and boundary conditions, thus more suitable for analysis of model uncertainty.