Abstract: As the backbone of China’s national water network gradually takes shape and its supporting infrastructure continues to improve, the focus of modern water-network development is shifting from physical connectivity to the coordinated deployment, effective operation, and continuous improvement of capabilities distributed across individual projects and facilities. In response to this shift, this study proposes a framework for system capability formation comprising three interrelated elements: “constraint-first specification, scenario-driven organization, and closed-loop implementation.” Constraint-first specification defines the boundary conditions governing the formation and deployment of system capabilities. Scenario-driven organization mobilizes the relevant capabilities of the engineering system, the operations management and scheduling system, and the intelligent regulation system around specific operational tasks. Closed-loop implementation establishes an operational feedback loop for verifying execution processes and task outcomes, enabling corrective adjustment, and ensuring that system capabilities are effectively exercised in practice. To operationalize this framework, three methods are developed: hierarchical capability decomposition, scenario-based classification and management of operational plans, and evidence-chain structuring. These methods yield three corresponding structured deliverables: a constraint-boundary package, a scenario-plan package, and an operational closed-loop package. An evaluation framework based on “evaluation specification–maturity grading–evidence chain” is then established to assess the extent to which system capabilities have been formed, identify specific weaknesses, and feed evaluation results back into the three structured deliverables. In this way, evaluation shifts from an end-of-process assessment to a guidance mechanism embedded throughout system capability formation, operational verification, and continuous improvement. The resulting framework links boundary definition, task organization, operational verification, and evaluation feedback, and provides a methodological basis for organizing, verifying, and continuously improving the system capabilities of modern water networks.