The recent development of high dikes to support rice production, upland crops, cattle rearing, and commercial aquaculture in the Vietnamese Mekong Delta has significantly diminished wild fish catch and aquatic animals that are important food sources for the poor. Changes to agro-ecological systems in An Giang Province during three periods are reviewed: before 1975, when a network of canals was established; during the Doi Moi policy reforms of the 1980s, when a rice-based farming system based on low or August dikes was introduced; and more recently, when a new farming system based on high dikes replaced the low dike system. This most recent transition occurred in parallel with the introduction of large-scale commercial aquaculture and the market economy. Under pressure from government targets and market forces, most farmers are now using the high dikes, fertilizers, pesticides, and pumping technology to produce three rice crops each year. However, the new production systems have severely reduced the habitat available to inland freshwater wild fish and other aquatic food resources. This has negatively impacted nutrition for many poor families who had depended on wild fish caught in the commons for much of their food and offers lessons for development of other tropical delta regions. This paper proposes a research agenda that would investigate the socioeconomic, nutritional, and water and energy use impacts of the changes in production systems that have occurred in rural communities in the Mekong Delta.