The river water surface profile serves as a fundamental basis for the construction of hydraulic engineering structures including levees, sluice gates, and pumping stations. In recent years, the river regime in the Middle and Lower Reaches of the Dongjiang River has changed greatly, and the extreme storm surges occur frequently in estuaries, resulting in a rising trend of the design tidal level. To study the water surface profile of the middle and lower reaches of the Dongjiang River and delta river network area under the new situation of changing boundary conditions, a one-dimensional hydrodynamic mathematical model is built based on MIKE11 software with the latest measured terrain data and design tide level. The floods in June 2022 and June 2020 are used to calibrate and verify the model. The water surface profiles of the middle and lower reaches of the Dongjiang River and the delta river network areas are calculated. The maximum water level error of calibration and verification of the model is within 0.1 m, and it can simulate the hydrodynamic conditions well. That the undercutting of the middle and lower reaches of the Dongjiang River leads to a downward trend in the water level under the same flow, and the rising design tidal level leads to the rise of water level in the lower reaches of the river network area.The change of water surface profile is in line with the actual situation. The research results can provide reference for the engineering design of embankment, water gate and pumping stations in the Dongjiang River and delta network river area.