The development history of the definition and connotation of water ecological health is systematically reviewed, and the commonly used models and methods to construct the index system for water ecological health assessment are sorted out. It is clarified that the index system for water ecological health assessment based on ecological integrity has the advantages of more scientific and comprehensive index classification, clearer work flow, and higher practicability and operability. Then, main difficulties of water ecological health assessment based on ecological integrity are pointed out, including the selection of indexes and benchmarks, the allocation of index weights, the identification of stressors, and the improvement of evaluation accuracy. The research is conducted so as to provide a clearer concept related to water ecological health assessment and decision-making support for evaluation of the effectiveness of water ecological protection and restoration.