“Determining development by water and acting within water constraints” is an inevitable requirement for water resources management in the new era. Water management adheres to the universal laws of existence, evolution, process, and reality. The systemic nature of water ecology dictates the importance of a systems perspective as the foundational philosophy and working method for water management practice. General Secretary Xi Jinping, using systems thinking to advance water conservancy development, has revealed the inherent relationship between water management and protection and state governance. Drawing on the water conservancy ideas of Marx and Engels, the ecological wisdom of water management and use in Chinese civilization, and the water management ethos of successive Chinese Communist Party (CPC) leaderships, General Secretary Xi Jinping uses quantitative and local descriptions to characterize the relational structure and functional coupling of water management, grasping the scientific methodology for water management in the new era through the organic unity of a dialectical perspective of time and space and practicality. The importance of systems dialectics in water conservancy development is explained based on the core connotations of the “defining city, land, population, and production by water” and the coupled synergy of “city-land-people-production”. Xi Jinping’s important principles of “defining city, land, population, and production by water” include “top-down” system planning, “bottom-up” system implementation, “differential synergy” system functional coupling, and “vertical integration” system dynamic regulation and control. These strategies embody the temporal allocation and spatial regulation in the process of water ecological governance. They are the methodological guidance of Xi Jinping’s Thought on Ecological Civilization on systems governance in terms of “temporal coordination” and “spatial layout”. They embody the characteristics of systems dialectics, such as integrity, hierarchy, self-organization, boundary nature, and practicality, forming an important strategic thought for national prosperity through water management in the new era.