In order to reveal the correlation between microbial diversity and the pollution degrees of the source water in a reservoir in Guangdong Province, for better understanding the ecological functions of this region, the environmental factors and microbial community were analyzed based on the characterization of the data from six sampling sites. The microbial diversity of different points was analysed, using PCR amplification technology and T-RFLP technology. Generally, the physical and chemical properties of each sampling point in the interstitial water in the reservoir showed obvious difference. Different forms of nitrogen concentrations and organic carbon concentrations in the reservoir were lower than those of the external diversion and the tributary. The concentrations of the enviromental factors were in the orders of wet season>dry season>normal season. The result showed that bacterial community structures varied considerably between the upstream and the downstream. The source water behaved the higher level of bacterial community diversity and richer degree in dry season than that in normal season and wet season. The dominant bacteria were Family1_uncultured, Bacteroidetes_uncultured, Sphingobacteriales_uncultured, Anaerolineaceae in normal season, Peptostreptococcaceae_incertae_sedis, Anaerolineaceae, SC-I-84, Xanthomonadales, and Clostridium in wet season, Rhodocyclaceae, Fusobacteriales, BSV26_norank, Comamonadaceae, Anaerolineaceae in dry season. Bacterial diversity was rich in the sediments in the reservoir. Correlation analysis showed that the microbial community structure was different at different sites, effected by environmental factors, among which the effects of different forms of nitrogen concentration were most obvious.