Bacterial community compositions of two neighboring freshwater lakes (i.e. Inner Sand Lake and Sand Lake in Wuhan, China) originating from one lake were studied by triplicate sampling based on Illumina Miseq sequencing. The pollutant concentrations in Sand Lake were twice as in Inner Sand Lake generally. Proteobacteria mainly containing Betaproteobacteria and Alphaproteobacteria were most abundant in the two lakes. The most dramatic differences at phylum level were that Inner Sand Lake had a higher proportion of Bacteroidetes while Sand Lake had a higher proportion of Cyanobacteria. The eutrophic Sand Lake had more taxa as for Alpinimonas, Flavobacterium, Lautropia, Pelomonas, Pseudomonas, Sphingorhabdus, Candidatus Aquirestis and Vogesella. On the contrary, the oligotrophic Inner Sand Lake had more taxa as for Aeromonas, Bradyrhizobium, Fluviicola, Limnohabitans, Luteolibacter, Polynucleobacter, Pseudarcicella and Sediminibacterium. Correlation network analysis revealed that Pseudarcicella, Sediminibacterium, Luteolibacter, Aeromonas in fresh lakes were potential bacterial indicators of good-quality lakes. Conversely, Flavobacterium, Pseudomonas and Candidatus Aquirestis seemed to be bacterial indicators of bad-quality lakes. Results obtained from this study could gain more knowledge on freshwater lake ecosystems from the bacterial aspect.