The quantity of the bacteria, especially the coliform group, in paddy water influenced the water quality and the matter circulation. However, there were few reports on that，especially under CO2 elevated condition. Therefore, by the aid of the internationally exclusive Free Air CO2 Enrichment of the rice-wheat sequential cropping system (started in 2004, located in Jiangdu county, Jiangsu province), this research did dynamic monitor on the population sizes of the bacteria and the coliform group, the concentrations of the total organic carbon (TOC) and the total nitrogen (TN) in paddy field water. The results showed that elevated atmospheric CO2 significantly increased the population sizes of the bacteria and the coliform group, as well as the concentrations of TOC and TN (P<0.01). Compared to the ambient plot, bacteria, coliform group, TOC and TN were respectively enhanced by 45.9%、68.8%、31.2% and 25.9% on average in FACE plot. There were significantly differences in bacteria population size, coliform group population size, water TOC and water TN between different rice growing stages (P<0.01). Those results demonstrate that atmospheric CO2 enrichment may aggravate the export of coliform group and bacteria from the paddy ecosystem to the surrounding wells and rivers through field drainage and rainstorms at the early stage of rice. Therefore elevated atmospheric CO2 may influence the rice security production and threaten human health.