The hydrogeomorphology of the Vietnamese Mekong Delta (VMD) has been significantly altered by natural and anthropogenic drivers. In this study, the spatiotemporal changes of the flow regime were examined by analysing the long-term daily, monthly, annual and extreme discharges and water levels from 1980 to 2018, supported by further investigation of the long-term annual sediment load (from the 1960s to 2015), river bathymetric data (in 1998, 2014 and 2017) and daily salinity concentration (from the 1990s to 2015) using various statistical methods and a coupled numerical model. Then, the effects of riverbed incision on the hydrology were investigated. The results show that the dry season discharge (i.e., in March-June) of the Tien River increased by up to 23% from the predam period (1980-1992) to the postdam period (1993-2018) but that the dry season water level at My Thuan decreased by up to −46%. The annual mean and monthly water levels in June at Tan Chau and in January and June-October at My Thuan in the Tien River decreased statistically, even though the respective discharges increased significantly. These decreased water levels instead of the increased discharges were attributed to the accelerated riverbed incision upstream from My Thuan, which increased by more than three times, from a mean rate of −0.16 m/year (−16.7 Mm 3 /year) in 1998-2014 to −0.5 m/year (−52.5 Mm 3 /year) in 2014-2017. This accelerated riverbed incision was likely caused by the reduction in the sediment load of the VMD (from 166.7 Mt/year in the predam period to 57.6 Mt/year in the postdam period) and increase in sand mining (from 3.9 Mm 3 in 2012 to 13.43 Mm 3 in 2018). Collectively, the decreased dry season water level in the Tien River is likely one of the main causes of the enhanced salinity intrusion.