Abstract: Backwater depths upstream of six bridges on the Nandu River in Hainan were estimated using MIKE21 and two empirical formulas in this paper, focusing on comparison of the calculations for floods of different frequencies. The results showed that the MIKE21 model was capable of simulating relatively complicated terrain with a higher accuracy: relative errors below 5% and coefficient RNS above 0.8 in calculations of model calibration and validation. And relative to the simulations, the estimates of D’Aubuisson formula and Henderson formula were smaller with the latter closer to MIKE21 for bridge piers of blockage factor less than 10%, while Luhao’s formula produces much larger backwater depths. Thus, when a bridge is located in a river channel with complicated terrain or the channel is crucial to flood control, a hydrodynamic model should be adopted to estimate the upstream backwater depth of a bridge for better accuracy in assessment of its effects on flooding.