This work addresses the multi‐objective design of water, energy and food supply systems in isolated rural communities using local resources. The approach used considers objective functions based on life cycle analysis such as water and carbon footprint, as well as economic performance considering the application and integration of normalized metrics to address the water‐energy‐environment‐food nexus. The results show that it is possible to build robust and accessible metrics for the analysis of problems with various design objective functions in decision‐making environments. The optimization problem considers decision variables associated with the sizing of units such as photovoltaic panels, wind turbines, thermal and electrical energy storage, wood‐fired boilers and the integration of food production systems involving aquaculture and local corn production. Water management is associated with domestic activities and crop irrigation.