The rise in global population and the consumption of energy, water, and food (EWF) resources continues to increase exponentially, placing enormous stresses on the three resource sectors. Therefore, assessing the inter-linkages between EWF resources is a very crucial step to achieve sustainable resource utilization, through increased economic efficiency and enhanced environmental performance. Such integrated assessment is often challenged by the difficulty in presenting a robust formulation which considers the necessary details of embedded systems, the availability of relevant models and data, as well as the representation of their uncertainties, based on which the design and operations of connected supply chains are ideally optimized. The objective of the research presented in this paper is to address the key challenges of the EWF nexus through the development of a techno-economic framework under non-cooperative settings. The methodology developed assumes a bottom-up approach in which the self-interested stakeholders, i.e. the players, are represented based on their own decision variables and objective functions at various levels, i.e. resources and environment systems, engineering systems, and their integration and operations. For this purpose, a combination of optimization models based on linear programming, stochastic programming, and game theoretic approach, represented by a Stackelberg competition, were developed. A case study is set in the State of Qatar with the objective of enhancing food security using hypothetical scenarios. The results obtained demonstrates that interesting interactions between systems, albeit competitive, can potentially result in the achievement of desired objectives under properly regulated markets, and is therefore envisaged as a promising contribution towards sustainable policy development and nexus governance.