Abstract: The urbanizing Yangtze River Delta is facing multiple water risks. The mass centralized hydraulic infrastructure combined with strict land-use regulation that has been implemented in recent decades to manage the flood risk is, however, challenged today by the need for more adaptive and ecological solutions. This research adapts the theory and method of delta urbanism to trace the long-term historical spatial evolution of the Yangtze River Delta from the perspective of dynamic interactions among the three subsystems: substratum, water management, and urbanization. In the five phases articulated by significant historical events, water management has played a changing role in the subsystems’ interactions: from being constrained to the substratum and from boosting urbanization to against urbanization. The significant difference in the change rate of the three subsystems is crucial in disturbing the balance between them. This historical review provides a multidisciplinary backdrop and perspective to integrating water management and spatial planning in the new Chinese territorial planning system. In particular, by reinterpreting local traditional water management methods, this retrospective provides a reference for the research and development of decentralized adaptive water management strategies and multiscale spatial planning and governance approaches.