The effects of natural disasters, pandemic‐induced lockdowns, and other disruptions often cascade across networks. In this work, we use minimum cost of resilience (MCOR) and operation‐based resilience metrics to quantify network performance against single‐connectivity failures and identify critical connections in interconnected networks. MCOR corresponds to the minimum additional infrastructure investment that is required to achieve a certain level of resilience. To guarantee MCOR, we incorporate the metrics in a multi‐scenario mixed‐integer linear program (MILP) that accounts for resilience in the design phase of interconnected networks. The goal is to obtain optimal generation and transportation capacities with flexible operation under all single‐connectivity disruption scenarios. We demonstrate the applicability of our resilience‐aware framework on a water‐energy nexus (WEN) example focusing on grass‐root design and retrofitting. We further apply the framework to analyze a regional WEN and observe that it is possible to achieve “full” resilience in the expense of additional regional investments.