Environmental monitoring is an important part of water ecological health evaluation. Traditional chemicalbased water quality monitoring usually provides only a few pieces of data, which could not reflect the reality state of the water body. Biologically oriented monitoring of the water environment directly responds to complex water conditions through the response of organisms to the environment, and occupies an important position in water health monitoring and assessment. To this end, this paper introduces conventional biological indicators in biomonitoring and summarises the environmental indicators of common indicator organisms including algae, invertebrates and fish in different types of polluted water bodies, based on pathogenic microorganisms and indicator organisms. The common methods for testing toxicity effects are introduced from the perspective of biotoxicity effects, and the responses of pollutants at different biological levels are analysed, thus indicating the advantages of the development of biotoxicity effects in the assessment of water environment health. The general approach to ecological integrity assessment and the application of emerging molecular biology techniques in water ecological health assessment are then described from the perspective of ecological integrity. It highlights the advantages of environmental toxicology and molecular biology in water environment monitoring, in order to provide support for more scientific and accurate water ecological health monitoring and early warning.