Vietnam is a major rice producer, and much of the rice grown is concentrated in the Red River Delta (RRD) and the Mekong River Delta (MRD). While the two deltas are highly productive regions, they are vulnerable to natural hazards and the effects of human-induced environmental change. To show that the processes and issues affecting food security are reinforcing, interdependent and operating at multiple scales, we used a systems-thinking approach to represent the major linkages between anthropogenic land-use and natural hazards and elaborate on how the drivers and environmental processes interact and influence rice growing area, rice yield and rice quality in the two deltas. On a local scale, demand for aquaculture and alternative crops, urban expansion, dike development, sand mining and groundwater extraction decrease rice production in the two deltas. Regionally, upstream dam construction impacts rice production in the two deltas despite being distally situated. Separately, the localized natural hazards that have adversely affected rice production include droughts, floods and typhoons. Outbreaks of pests and diseases are also common. Climate-change-induced sea level rise is a global phenomenon that will affect agricultural productivity. Notably, anthropogenic developments meant to improve agricultural productivity or increase economic growth can create many unwanted environmental consequences such as an increase in flooding, saltwater intrusion and land subsidence, which in turn decreases rice production and quality. In addition, natural hazards may amplify the problems created by human activities. Our meta-analysis highlights the ways in which a systems-thinking approach can yield more nuanced perspectives to tackle “wicked” and interrelated environmental challenges. Given that deltas worldwide are globally significant for food production and are highly stressed and degraded, a systems-thinking approach can be applied to provide a holistic and contextualized overview of the threats faced in each location.