In order to improve the purification effect of ecological floating beds, the carbon source composite fillers with corncob and zeolite were applied to three plant assemblages, i.e. Acorus calamus L. + Cyperus altenifolius, Canna indica L. + Cyperus altenifolius, and Canna indica L. + Acorus calamus L.. With the non-carbon fillers as the control, we investigated the removal effect of nitrogen, phosphorus and organic matter by the biomass carbon source composite fillers, as well as the growth characteristics of the plants. The results showed that the composite carbon source filler played an important role in the purification process of the floating beds and enhanced the plant growth. The average growth rate and quantity of all three plant assemblages with carbon source composite fillers were better than those with non-carbon fillers in general. The average removal rate of ammonia nitrogen (NH4+—N), nitrate nitrogen (NO3-—N), total phosphorous (TP) and chemical oxygen demand (COD) by these three plant assemblages were 73.0%, 88.7%, 54.4% and 58.7%, respectively, which were improved by 6.9%, 5.0%, 18.4% and -22.3% respectively, compared to those of the non-carbon fillers. The assemblage of Acorus calamus L. + Cyperus altenifolius with a biomass carbon source filler could remove NH4+—N、NO3-—N、TP by the average rate of 76.6%, 92.6%, and 60.7% respectively, which was evidently better than the removal result of Canna indica L. + Acorus calamus L., and Canna indica L. + Cyperus altenifolius. Therefore, the assemblage of Acorus calamus L. + Cyperus altenifolius with a biomass carbon source filler is recommended for the in-situ water restoration.