Abstract: From the perspective of systems science, this article systematically examines the multi-layered systemic characteristics of river systems and river governance. It argues that river systems are typical natural geographical systems, exhibiting integrated features of morphological systems, cascading systems, process–response systems, and control systems. These characteristics reflect the holistic and dynamic nature of river systems, in which matter and energy are transferred along upstream–downstream and main–tributary networks, continuously driving their evolution. On this basis, human development and utilization of rivers—through reservoirs, dams, and inter-basin water transfer projects—further transform river systems into civil engineering systems with clear objectives, autonomy, and constraints, exerting profound impacts on river morphology, hydrological processes, ecological environments, and social structures. The article further emphasizes that river governance is not a matter of isolated projects or single factors, but a complex multi-variable, multi-mechanism system involving natural, engineering, economic, social, and ecological elements. The overall system state is determined by direct and indirect interactions among elements, feedback mechanisms, and their fully coupled pathways. Through analysis of system structures and mechanism pathways, the author highlights that effective river governance must adopt a systems-thinking approach: clarifying governance objectives, constructing a comprehensive system framework, accurately identifying key elements and their interactions, and closely monitoring system evolution trends. Only under an integrated, coordinated, and forward-looking governance framework can river systems evolve toward sustainable harmony between humans and nature.