Abstract: In order to explore the changes of microbial community structure in the sediments of the tidal reach of the Taojiang River during the normal water period and low water period, the high-throughput sequencing technology of 16S rRNA gene was used to analyze the microbial community structure and diversity characteristics of sediment samples from different stations in each period. The results showed that among the physicochemical properties of the water body in the tidal reach of the Taojiang River, ammonia nitrogen exhibited significant spatial and temporal heterogeneity, total nitrogen (TN) pollution was relatively serious, and total phosphorus (TP) was generally low. The microbial community richness in the sediments during the normal water period was higher than that during the low water period. The microbial community structures in the sediments during the normal water period and low water period were highly similar, with the differences mainly reflected in the relative abundance fluctuations of the main dominant bacteria in different river sections. At the phylum level, Chloroflexi, Proteobacteria, Acidobacteriota, Bacteroidota, Nitrospirota, and Actinobacteriota were the main dominant bacteria in the sediments during both periods. At the phylum level, NB1-j was unique to sediments during the normal water period, while Firmicutes was unique to sediments during the low water period. At the genus level, the sediments in the normal and dry seasons were mainly composed of Nitrospira, Sva0485, BSV26, and Latescibacterota. Among them, TRA3-20 and RB41 were unique to sediments during the normal water period, while SC-I-84 and bacteriap25 were unique to sediments during the low water period. The relative abundances of the main dominant bacteria at each station showed small temporal differences but large spatial differences. Meanwhile, combined with the bacterial characteristics of the flora, the succession patterns of dominant bacterial communities under different seasons and river sections were explored, which provided a reference for the ecological management strategies of the tidal reach of the Taojiang River.