Waterway and canal systems are particularly cost effective in the transport of bulk and containerized goods to support global trade. Yet, despite these benefits, they are among the most under-appreciated forms of transportation engineering systems. Looking ahead, the long-term view is not rosy. Failures, delays, incidents and accidents in aging waterway systems are doing little to attract the technical and economic assistance required for modernization and sustainability. In a step toward overcoming these challenges, this paper argues that programs for waterway and canal modernization and sustainability can benefit significantly from system thinking, supported by systems engineering techniques. We propose a multi-level multi-stage methodology for the model-based design, simulation and formal verification of automated waterway system operations. At the front-end of development, semi-formal modeling techniques are employed for the representation of project goals and scenarios, requirements and high-level models of behavior and structure. To assure the accuracy of engineering predictions and the correctness of operations, formal modeling techniques are used for the performance assessment and the formal verification of the correctness of functionality. The essential features of this methodology are highlighted in a case study examination of ship and lock-system behaviors in a two-stage lock system.