The water-energy-food (WEF) nexus has motivated several studies, opening space to provide robust support for the decision-making process. Certain studies seek to understand the interdependence of these three resources in a quantitative and/or qualitative manner, usually using total water, energy, and food indicators. However, in times of social, economic, and environmental crisis, national policies must be optimized, and hence it is necessary to evaluate marginal and critical indicators of each resource, i.e., sensitive indicators. Based on these indicators, we propose a methodology for assessing ecological efficiency (eco-efficiency) in industries using a multiregional input-output table, Data Envelopment Analysis, and the Malmquist index, with the main objective of internalizing normally overlooked impacts in the national policymaking process. For this, we present a quantitative assessment of the WEF nexus in the Brazilian food and beverage industry, since it is one of the pillars of the country's economy and has several positive and negative effects related to the WEF nexus, as well as a growth trend to meet rising food demand. From 2015 to 2019, this industry eco-efficiency was evaluated in terms of water stress, fossil energy consumption, and financial compensation to low-skilled workers. The main findings show that the Fish industry has the highest average eco-efficiency, with sustainable gains over the period, while the Meat cattle industry has the lowest average eco-efficiency. As a result, the Fish industry places less strain on these resources to generate the same socioeconomic benefits as others, resulting in less food and water insecurity, and should be prioritized in Brazil's national policies regarding industry expansion. We conclude that this methodology can help integrate WEF resources into national policy decision-making processes, allowing the identification of negative impacts that should be avoided or mitigated, as well as positive impacts that should be encouraged.