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This study aimed to examine the bacterial communities present in the macrophyte- (MDZs) and algae-dominated zones (ADZs) of the Chengdong Lake, by utilizing high-throughput sequencing techniques. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the two lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The results obtained through the analysis of Shannon indices indicated that the biodiversity of water samples in the ADZs was greater compared to the MDZs. However, no statistically significant difference was observed in sediment samples across different regions of the lake. Our findings indicate that Cyanobacteria phylum abundance was highest in the ADZs, while the MDZs had Proteobacteria as the most abundant phylum, comprising over 30% of the bacterial community. The db-RDA analysis revealed that total nitrogen (TN) and total phosphorus (TP) in the water, as well as organic matter (OM) in the sediment, were the primary environmental factors influencing the variation in bacterial communities. This study contributes fundamental data towards comprehending the diversity variation of bacterial communities across different habitats within Chengdong Lake.