Water quality system informatics (WQSI) is an emerging field that employs cybernetics to collect and digitize data associated with water quality. It involves monitoring the physical, chemical, and biological processes that affect water quality and the ecological impacts and interconnections within water quality systems. WQSI integrates theories and methods from water quality engineering, information engineering, and system control theory, enabling the intelligent management and control of water quality. This integration revolutionizes the understanding and management of water quality systems with greater precision and higher resolution. WQSI is a new stage of development in environmental engineering that is driven by the digital age. This work explores the fundamental concepts, research topics, and methods of WQSI and its features and potential to promote disciplinary development. The innovation and development of WQSI are crucial for driving the digital and intelligent transformation of national industry patterns in China, positioning China at the forefront of environmental engineering and ecological environment research on a global scale.