To explore the bacterial community structure and its relationship with environmental factors, the water and sediment in the purification channel of aquaculture tailwater in the Tiaozini reclamation area were monitored. The results showed that there were significant differences in water quality between different months and physicochemical properties of sediments at different sites. Judging by the total nitrogen (TN) and total phosphorus (TP), the river water was at a level of eutrophication, but it met the second-level discharge standard of water from aquaculture ponds in Jiangsu Province. Olsen-P indicated that the sediments were not at a high nutrient level. The changes of bacterial community composition in water and sediments were consistent with physicochemical properties, and significant differences were found in the diversity, richness, and composition of bacterial communities in the two environments. Cyanobacteria was one of the dominant bacteria in water, with a relative abundance of 39.33% in September. Cyanobium_PCC-6307 occupied the highest abundance in both water (13.34%) and sediments (8.15%) and had the greatest effect on bacterial communities. Water temperature (T), TN, soluble active phosphate (SRP), and permanganate index (COD_Mn) were significantly correlated with bacterial communities. Except TN, the other 3 indicators were positively correlated with Cyanobium_PCC-6307. Water soluble phosphorus (WSP), readily desorbable phosphate (RDP), and total carbon (TC) in the sediments were significantly correlated with bacterial communities, and WSP and RDP were positively correlated with Cyanobium_PCC-6307. To limit the accumulation of Cyanobium_PCC-6307 in the channels, the control of phosphorus in aquaculture tailwater should be strengthened. This study provides a reference for the regulation of tailwater and healthy development of aquaculture in coastal reclamation areas.