To analyze the water quality of the Fu River, nine sampling sites were chosen from Baopingkou site in Dujiangyan to Wangjiang Park site in Fu River. Three microbiological indexes, including total number of bacteria, total coliform and the number of fecal coliform, have been selected to evaluate the water quality, analyze seasonal factors and find out the contamination sources in two different seasons. Besides, taking the antibiotic resistance rate of Escherichia coli at Baopingkou as background, 102 E. coli identified by morphology and 16S rDNA have been selected for following antimicrobial susceptibility testing, and the susceptibility has been performed according to the standard disk diffusion K-B method. The results show that though the total number of bacteria, total coliform and fecal coliform varied from Baopingkou, Dujiangyan to Wangjiang Park, the total number of bacteria shows an increasing trend as the water flows. The nutrients enrich in spring and summer, and water quality decrease. The susceptibility of 13 antimicrobial agents tested against E. coli isolated shows that 0.96% 33.33% of the isolates are resistant to β-lactam, 1.39% 7.84% to aminoglycoside, 11.43% 11.76% to fluoroquinolone, and 52.78% to trimethoprim-sulfamethoxazole. The resistance to β-lactam and fluoroquinolone is related with the source of water, however, other resistances are in connection with polluted water discharged from hospital and residential areas. Generally, this study has provided theoretical foundation for the control of pollution in Fu River.