Aquatic ecological monitoring and assessment in freshwater ecosystems centers on the effective management, protection, and sustainable utilization of freshwater resources. In the past several decades, the management policies in developed countries such as the United States and those in Europe had emphasized the ecological integrity of freshwater ecosystems. Accordingly, a series of research plans and programs had been successively launched for systematically monitoring and evaluating status of freshwater ecosystems using biological communities as core indicators. However, the monitoring and assessment systems in China are mainly based on traditional physical and chemical indices, thus lacking biological indicators to illustrate changes in ecological quality of freshwater ecosystems. Therefore, the progress of water quality improvement cannot meet the long-term goals and overall requirements of the "14th Five-Year Plan" for water environment management-a conceptual change from water pollution prevention and control to a unified framework of "water resource, water ecology, and water environment (i.e., three waters)". In this review, we systematically discussed the experience of monitoring and assessment philosophy and operational techniques and applications of watershed management in developed countries/regions, such as the United States, Australia, and European Union. In addition, we further summarized the existing works of aquatic ecological monitoring and assessment in China, analyzed key issues that restrict the current water ecological monitoring and assessment progress, and finally proposed relevant suggestions for systematically developing aquatic ecological monitoring and assessment systems in China, including protection target, management mode, monitoring network, scientific research, public participation. It would provide decision support and crucial reference for accurately assessing quality of the nationwide freshwater ecosystems and further evaluating the effectiveness of protection and restoration in China.