<p>This work-in-progress paper proposes a design methodology that addresses the complexity and heterogeneity of cyber-physical systems (CPS) while simultaneously proving resilient control logic and security properties. The design methodology involves a formal methods-based approach by translating the complex control logic and security properties of a water flow CPS into timed automata. Timed automata are a formal model that describes system behaviors and properties using mathematics-based logic languages with precision. Due to the semantics that are used in developing the formal models, verification techniques, such as theorem proving and model checking, are used to mathematically prove the specifications and security properties of the CPS. This work-in-progress paper aims to highlight the need for formalizing plant models by creating a timed automata of the physical portions of the water flow CPS. Extending the time automata with control logic, network security, and privacy control processes is investigated. The final model will be formally verified to prove the design specifications of the water flow CPS to ensure efficacy and security.</p>