Understanding the relationship between functional and species diversities as well as their association with habitat heterogeneity can help reveal the mechanisms of species coexistence in ecological communities. However, these interactions have been poorly studied in freshwater ecosystems. In this study, we evaluated the spatio-temporal dynamics of functional diversity and traditional species diversity indices, and the relationships between them. The main results were as follows:In the space sequence, species diversity indices were the lowest in reach B, and the results showed that intermittent disconnection had a significant influence on species diversity. Functional richness was the highest in reach D and the lowest in reach A, functional evenness was highest in reach A, and functional divergence was the highest in reaches A and B and the lowest in reach D. In the time series, the lowest mean value of species richness and Shannon index were recorded in October and the highest in April, and the evenness index was the lowest in December and the highest in October. The three functional diversity indices were significantly different and orthogonal among seasons, and they were mainly affected by hydrological conditions and benthic animal life history. Correlation analysis was used to analyze the relationship of the biodiversity indices, and the results showed no significant correlations among functional diversity indices. Functional richness was significantly correlated with species richness and Shannon index and also with functional evenness and species evenness. Stepwise regression analysis was used to analyze the influence of species diversity on functional diversity, and the results showed that functional richness was significantly affected by species richness and Shannon index, and also by functional evenness and species evenness. Furthermore, we also found that the fitting degrees among this indices were not high. By further analysis and discussion, we found that compared to species diversity, functional diversity was more comprehensive in revealing habitat gradient.