Abstract: Diatoms play a vital role in aquatic ecosystems. They are widely used in water quality monitoring because of their wide distribution, short reproductive cycle and sensitivity to environmental variations. To establish the diatom indexes suitable for ecological water assessment in China, we investigated diatom community structure and environmental characteristics in the main lakes and the lower reaches of the Yangtze River and the Qingyi River from August 2017 to August 2018. Spearman correlation analysis and box-plot were utilized to explore the relationships between diatom indexes and environmental factors, and to test the applicability of diatom index. The results showed that: (1) By studying the relationship between diatoms and environmental factors in the main lakes and the lower reaches of the Yangtze River and the Qingyi River, we determined the optimal values, tolerance values and environmental indicators of 114 diatoms to the changes of total phosphorus, chemical oxygen demand and total nitrogen, and established a comprehensive diatom index suitable for the environmental assessment of lakes in the lower reaches of the Yangtze River and Qingyi River. (2) Spearman correlation analysis showed that the Comprehensive Diatom Index (CDI) was significantly correlated with the total phosphorus, chemical oxygen demand, total dissolved solids and total nitrogen in rivers and lakes. (3) The Box-plot results showed that the CDI value increased gradually with the gradience of water quality in rivers and lakes, indicating CDI can reflect the environmental quality of the waters. The results suggested that CDI is a good biological evaluation index for water quality of lakes in the lower reaches of the Yangtze River and Qingyi River.