Endophytic bacteria were isolated from Canna indica, and three strains C01, C16 and C20 were screened out regard to their abilities of producing indoleacetic acid (IAA) and siderophore, nitrogen fixation, as well as phosphate solubilization. The aim of this study is to evaluate the influence of inoculating of endophytic bacteria on seed germination and seedling growth of C. indica, and to evaluate the removal rates of nutrients in water body by C. indica inoculated with endophytic bacteria in the pilot scale floating bed treatment system. The results showed that C01, C16 and C20 promoted the germination of seed and growth of plants. The germination rate of C16 treatment was 83.3%, significantly higher than that of the control, which was 31.1%. During the water purification experimental stage, the removal rates of total phosphorus and total nitrogen in the C16 treatment were 88.4% and 96.9%, respectively, which were 26.4% and 15.6% higher than the control. At the end of the experiment, the biomass and root length of the C01 and C16 treatment were significantly higher than the control, the soluble sugar content and soluble protein content in the C16 treatment were 317.3% and 97.8% higher than those in the control respectively. C01, C16 and C20 were proved to be Pseudomoanas fluorescens, Enterobacter sp., Erwinia sp. based on 16S rRNA sequence analysis.