This paper employs historical analysis, policy text research, and practical case studies to systematically examine the historical evolution of river and lake management in China, as well as the reform and innovation measures adopted in the new era. It summarizes the experiences gained from river and lake management practices in the new era and, by applying theories such as ecosystem services, sustainable development, collaborative governance, and public participation, proposes the transformation directions and implementation pathways for river and lake management in China. Research indicates that China has always attached great importance to the development of river and lake management. Currently, guided by the new development philosophy and General Secretary Xi Jinping’s important discourses on river and lake management, China has promoted the implementation of the River and Lake Chief System, the national strategy for major rivers and the national water network, and the creation of Beautiful and Happy Rivers and Lakes. These practices have collectively shaped a set of reform experiences suited to the new era in river and lake management: adhering to the guidance of Xi Jinping’s ecological civilization thought, leveraging the advantages of the national system for accomplishing major tasks, fully utilizing the role of the River and Lake Chief System, consistently upholding the concept of systematic governance, continuously strengthening the river and lake supervision system, and vigorously enhancing the application of new technologies. In the new era, river and lake management needs to achieve five major transformations: from focusing primarily on river and lake project construction to emphasizing river and lake resource allocation, from river and lake development and utilization to ecological rejuvenation, from government-dominated management of rivers and lakes to societal participation in management, from focusing on river and lake health to the construction of Beautiful and Happy Rivers and Lakes, and from traditional river and lake management to the realization of the value of ecological products. These transformations aim to further enhance the effectiveness of river and lake management, achieve harmonious coexistence between humans and nature, and ensure the sustainable utilization of river and lake functions.