Indices of biotic integrity (IBIs) are widely used to assess aquatic ecosystem health. However, there are few studies on their relationships. Based on fish, macroinvertebrate and plankton survey data collected in the Ganjiang River system from 2016 to 2017, redundancy analysis (RDA) and canonical correspondence analysis (CCA) were used to analyze how the community structures of these organisms respond to environmental variables. The fish IBI (F-IBI), benthic macroinvertebrate IBI (B-IBI), and phytoplankton IBI (P-IBI) were applied to evaluate the health status of the aquatic ecosystem. A Kruskal–Wallis test (p < 0.05) and Spearman’s correlation coefficient analysis were performed to evaluate the spatiotemporal heterogeneity of the results. Our results suggested that the F-IBI-, B-IBI-, and P-IBI-based assessments indicated good, fair, and healthy Ganjiang River system ecosystem health statuses, respectively, and significant differences existed among these indices (p < 0.05). The main environmental factors affecting F-IBI, B-IBI, and P-IBI were different. At the temporal scale, the F-IBI and B-IBI were stable, while the P-IBI fluctuated obviously. The consistency between the F-IBI and B-IBI results was better than that between each of these indices and the P-IBI results, and the consistency was better on a larger scale. These research results show that comprehensive assessments based on multiple groups rather than a single group can better characterize the impacts of environmental pressures on water ecosystems.