Study region: The Mekong basin, where climate change and anthropogenic interventions (e.g., dams, sand mining, and sluice gates) have intensified in the recent decades affecting the pristine flow regime and salinity intrusion. Study focus: This paper aims at quantifying the flow regime alterations in the entire Mekong from 1980 to 2015 and linking with the controlling drivers of alterations. In this regard, various indicators, analytical methods, and a semi two-dimensional hydrodynamic and advection-dispersion model were used. New hydrological insights for the region: The flow regime alterations in the high-dam development period (2009–2015) are more pronounced than in the low-dam development period (1993–2008), compared to the no-dam development period (1980–1992), based on most of the indicators analyzed. In the high-dam development period all existing dams with large reservoir capacity seemed to have cumulatively reduced the flood pulses and frequency and increased the low-flow discharge along the entire Mekong through reservoir operations, exceeding climate change effect. In the recent years the water levels in the low-flow season in the Vietnamese Mekong Delta (VMD) have decreased, possibly because of increased riverbed incision caused by reduced sediment supply and increased sand mining. The reduced water levels together with the increased number of the sluice gates constructed seemed to have increased salinity intrusion in the VMD which may be partly reduced by early emergency water release from upstream dams.