A dense dike system has been built in the upstream floodplains of the Vietnamese Mekong Delta, allowing large scale rice production based on compartmentalized fields and optimized water management. Intensive cultivation has enabled farmers to greatly increase their rice productivity and augment the national food bowl. However, flood-control structures have undermined the water retention capacity, compromising various benefits of floodwaters for delta ecosystems. Effects are both internal and external to farming. Negative internal effects are the large investment requirements and higher farming costs. Negative externalities include increased flood damage, reduced sediment flows, saltwater intrusion and riverbank erosion. In this study, we assessed the effects of three dike–agricultural system scenarios on delta-level sustainability, considering both internal and external effects. Direct and indirect costs were estimated using various methodologies and the literature. Our findings show that extensive development of high dikes on the floodplains is the least economical and most ecologically risky alternative. In this scenario, accelerated high-dike construction exacted a cost 136% greater than the situation represented by the baseline year of 2011. Externalities in this scenario contributed to rising economic losses in both aquaculture and agriculture. The scenario of transforming high-dike into low-dike systems revealed lower water management costs combined with lesser environmental impacts and greater capacity to exploit floodwater benefits. Our findings provide a useful input for decision-makers considering the unintended economic consequences of existing water management strategies. They support a transition to low-dike farming systems for a more sustainable delta.