In this study, we analyzed the characteristics of the bacterial community in Nanchang section of the Ganjiang River, Lake Poyang Basin, based on monthly sampling on five sites (G1-G5) from April 2015 to March 2016. G1 lays on the Ganjiang River before entering the urban region, G2 in the center of the city, and G3-G5 in the three branches leaving the urban region, respectively. The hydrometeorological factors (air temperature and flow rate) were recorded; the hydrochemical factors of sampling water, including nutrients (dissolved organic carbon, total phosphorus and ammonium nitrogen), ions (HCO₃^-, Cl^-, NO₃^-, SO₄^2-, Na⁺, K⁺ and Mg²⁺), and heavy metals (Mn, Cd, Cr, Pb, Cu, As, Ba and Fe) were measured. The bacterial community was characterized using Illumina high-throughput sequencing. Nonmetric Multidimensional Scaling (NMDS) was carried out on OTUs data using Bray-Curtis distance matrices to examine the difference in bacterial community between water samples. The ‘Bioenv’ in the R package ‘Vegan’ and redundancy analysis was used to explore the influence of environmental factors on the bacterial community in the river. The SourceTracker Model, which was based on Bayesian Statistical Method, was used to estimate the change of bacterial community in Nanchang section of the Ganjiang River. Results showed that:The dominant phyla were Actinobacteria (34.05%) and Proteobacteria (31.59%), followed by Firmicutes (15.49%) and Bacteroidetes (9.12%). Air temperature and flow rate were the main environmental factors influencing bacterial communities in the river. The optimal single-parameter for explaining the variance of OTU abundance was air temperature, and the optimal single-parameter for explaining the variance of phylum abundance was flow rate. The influence of hydrometeorological factors (air temperature and flow rate) on bacterial communities was higher than that of the water chemistry. Except for Proteobacteria, there was no significant difference of the bacterial community between the five sampling sites. The results of SourceTracker Model showed that the influence of Nanchang city on the bacterial community in the Ganjiang River ranged from 6.33% to 34.67%, and the influence on bacterial community in the south branch of the Ganjiang River was significantly higher than that in other river sections. The influence of Nanchang city on bacterial community was small, and the main influenced phylum was Proteobacteria.