In recent years, i.e., in 2016 and 2020, large-scale saltwater intrusion has been causing shortage of freshwater for domestic and agricultural uses in the Vietnamese Mekong Delta. Therefore, sufficient understanding of the impact factors on saltwater intrusion in the delta is important for water resources management. This paper examines the effects of reduced water flow by upstream dams’ operation and river bed incision on saltwater intrusion in the Mekong Delta. In that regard, long-term water flow at two upstream hydrology stations from 1980 to 2020 and river bed incision from 2009 to 2017 were analyzed. Then, one-dimensional hydrodynamic and advection-dispersion model was used to compare salinity concentration and intrusion length between three scenarios. The results indicated that the influence of river flow on saltwater intrusion is more significant than that of river bed incision. When river flow at Kratie reduced by 14,4%, the highest salinity concentration (S) and intrusion length (L) increased by 17.4% and 10.5%, respectively. While, river bed incised by 0.88m for the next four years, S and L increased by 2.8% and 1.67%, respectively.