Abstract: Inland water ecosystems, as a vital component of Earth's biosphere, provide essential ecosystem services upon which human society depends for survival and development. Their native species form the fundamental basis of these ecosystem service functions. Against the backdrop of global environmental change and intensifying human activities, inland water ecosystems are facing unprecedented pressures and challenges across various spatial scales, including global, basin-wide, and regional levels. Therefore, scientifically and accurately understanding the integrity of inland water ecosystems holds significant theoretical value and practical importance for formulating effective ecological and environmental governance, protection strategies, and measures. This paper systematically reviews the evolution and development of the integrity concept, proposes a scientific definition of inland water ecosystem integrity, and constructs a conceptual framework for its application. This framework includes core components such as scale definition, conceptual model development, key indicator selection, quantitative assessment, and adaptive management, aiming to provide a perspective for the systematic practice of water ecosystem integrity. Ecosystem integrity is not only a crucial concept for understanding aquatic ecosystems but also an effective tool for implementing watershed systematic governance. Given the complexity, uncertainty, and dynamic nature of inland water ecosystems, future efforts necessitate strengthened interdisciplinary collaboration, continuous improvement of theoretical frameworks, innovation in technical methodologies, and the promotion of further implementation of the ecosystem integrity concept in watershed governance.