Building high dykes is a common measure of coping with floods and plays an important role in agricultural management in the Vietnamese Mekong Delta. However, the construction of high dykes causes considerable changes in hydrodynamics of the Mekong River. This paper aims to assess the impact of the high-dyke system on water level fluctuations and tidal propagation in the Mekong River branches. We developed a coupled 1-D to 2-D unstructured grid using Delft3D Flexible Mesh software. The model domain covered the Mekong Delta extending to the East (South China Sea) and West (Gulf of Thailand) seas, while the scenarios included the presence of high dykes in the Long Xuyen Quadrangle (LXQ), the Plain of Reeds (PoR) and the Trans-Bassac regions. The model was calibrated for the year 2000 high-flow season. Results show that the inclusion of high dykes changes the percentages of seaward outflow through the different Mekong branches and slightly redistributes flow over the low-flow and high-flow seasons. The LXQ and PoR high dykes result in an increase in the daily mean water levels and a decrease in the tidal amplitudes in their adjacent river branches. Moreover, the different high-dyke systems not only have an influence on the hydrodynamics in their own branch, but also influence other branches due to the Vam Nao connecting channel. These conclusions also hold for the extreme flood scenarios of 1981 and 1991 that had larger peak flows but smaller flood volumes. Peak flood water levels in the Mekong Delta in 1981 and 1991 are comparable to the 2000 flood as peak floods decrease and elongate due to upstream flooding in Cambodia. Future studies will focus on sediment pathways and distribution as well as climate change impact assessment.