Taking the typical inflow river of Poyang Lake, Raohe River, which is affected by human activities such as mining, as the research object, the 16S rRNA gene amplification sequencing technology was adopted to analyze the distribution characteristics and influencing factors of the bacterial communities in the sediment of the inflow section of Raohe River, the north branch Changjiang River and the south branch Le’an River. Corresponding biomarkers were also identified. The results showed that the bacterial α-diversity in the inflow section of the sediment was lower than that in Changjiang River and Le’an River, and there were significant differences in the bacterial community structures of different river sections. The complexity of the sediment bacterial co-occurrence network in the inflow section was lower than that in Changjiang River and Le’an River, while the abundance of key species in Le’an River was higher than that in Changjiang River and the inflow section. There was a significant attenuation relationship between the bacterial community and environmental factors, geographical distance, and bacterial community structure was affected by both environmental and geographical factors. Environmental factors had a greater impact on the bacterial community than geographical factors. Heavy metals had the highest explanatory rate of bacterial community structure and key species, which are 11.2% and 8.7%, respectively. Heavy metal and nutrient salt combined pollution, especially heavy metal pollution, led to a significant reduction in bacterial α-diversity and the complexity of co-occurrence patterns. Acidobacteria class and Bacillaceae class were identified as biomarkers of heavy metal pollution in the sediment of Raohe River.