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Ho Chi Minh City gets severely inundated by upstream flooding and a combination of rising spring tides and rain, owing to the combined impacts of rapid urbanization and sea level changes. A sea dike to close Can Gio Bay has been proposed to regulate storage and control water levels in the drainage and sewer system of Ho Chi Minh City. However, this proposed sea dike and different gate operating modes could significantly change the hydrodynamic regime in Can Gio Bay. In this study, a two-dimensional hydrodynamic model was developed to assess changes in the hydrodynamic regime after construction of the sea dike, including fluctuations in the inundated areas in Can Gio Bay mangrove forests. The results show that sea dike construction is an effective solution for controlling water levels and reducing inundation, especially considering a sea level rise scenario in the year 2050. Further, the gate operation mode also affects the effectiveness of inundation reduction, which is approximately 10% better than the same sea dike type without gate operation. However, the sea dike was less effective in a sea water level rise scenario in 2100 for all scenarios.