The economic reform “Đổi Mới” in 1986 has rapidly increased the number of craft villages in Vietnam, especially in the Red River Delta (RRD) leading to environmental degradation. This article presents an assessment of environmental and resource issues of agro-Food Processing Craft Villages (FPCVs) in RRD using a refined approach to material flow analysis focusing on consistent quantification of uncertainty with particular attention to secondary and empirical data that are often faced in material flow analyses in transition economies. Material flows of agro-Food Processing including eight types of production were examined and linked to activities of private Households, Rice Cultivation, and Pig Farming in a model called Red River Delta. Materials investigated were Goods (i.e., total materials), organic carbon (org.C), nitrogen (N), and phosphorus (P). The findings reveal material cycles are almost entirely open, that is, the materials used in FPCVs do not recycle within the region. From ∼10.5 million tons/year of imported Goods used for agro-Food Processing, final products and utilized materials account for minor fractions (∼5%, by weight). Conversely, the majority (88%) is directly discharged. Materials accumulated as stocks represent 1% of Goods (100,000 tons/year), 21% of org.C (∼34,000 tons/year), 42% of N (∼1,300 tons/year), and 57% of P (∼300 tons/year), whose substance concentrations vastly exceed natural resilience capacities. Although agro-Food Processing accounts for negligible material shares in Red River Delta, FPCVs pollution is severe at local levels due to the location of home-based production. Several options for closing material loops at various system scales are recommended for environmental and resource management of FPCVs. The material flow analysis results provide a database that may be used as a decision support tool for production establishments in craft villages and relevant authorities in setting priorities on environmental planning and resource management. © 2019 The Authors. Journal of Industrial Ecology published by Wiley Periodicals, Inc. on behalf of Yale University