By examining basin-wide simulations of a river regime over 83 years with and without dams, we present evidence that climate variation was a key driver of hydrologic variabilities in the Mekong River basin (MRB) over the long term; however, dams have largely altered the seasonality of the Mekong’s flow regime and annual flooding patterns in major downstream areas in recent years. These findings could help us rethink the planning of future dams and water resource management in the MRB.