River ecosystems are facing a deepening biodiversity crisis. Developing robust biotic indicators to assess ecological status across large spatial scales are important. In the subtropical Liuxi River of southern China, 34 fish indicators, including 4 genera and 30 species, were selected from 108 fish species by linear discriminant analysis. These indicators were combined into 18 groups and assigned scores according to their species-specific requirements for food resources and habitat patterns. The ecological and trophic functioning of optimized indicators can reflect not only the community diversity and food web properties but also the environmental quality of the ecosystem. Three formulas for calculating the index of fish indicators ( IFI) were developed based on the scoring of each indicator and weighted by relative abundance (individual number, i.e., IFI_N) and relative biomass (wet weight, i.e., IFI_B). Spearman correlation analysis showed that IFI_B exhibited a more powerful explanation of biodiversity and environmental factors than IFI_N and unweighted IFI. Therefore, we conclude that IFI_B has absolute advantages in constructing an indicator-based environmental evaluation system since it contains comprehensive information on biology and ecology. In the future, the application of indicator scoring methods can contribute greatly to the conservation and development of aquatic ecosystems.