The present experiment tested various EFBs for the purification of hypereutrophic waters under batch and continuous flow conditions. A conventional plant-only EFB (EFB-PO) was used as the control system and compared to EFBs using either rice straw (EFB-RS) or plastic filling (EFB-PF) as a substrate for microorganisms. Under the batch condition, the mean removal rates of the EFB-RS for total nitrogen (TN), ammonium nitrogen (NH4+-N), and nitrate nitrogen (NO3−-N) were, respectively, 76.94, 93.50, 93.18% after 2 days, which represent increases of 43.94%, 19.83%, 75.24% and 34.76%, 24.67%, 34.54% over the same values for EFB-PF and EFB-PO, respectively. The number of total bacteria, nitrifying bacteria, and denitrifying bacteria in the rice straw system, as well as the total amount of biomass, was significantly greater than in the plastic filling system. The results of the continuous flow experiment indicated that the mean removal rates of TN, NH4+-N, and NO3−-N for EFB-RS and EFB-PF were, respectively, 72.21%, 88.88%, and 80.41%, and 51.85%, 86.23%, and 58.62% when the hydraulic retention time (HRT) was 24h. Relative to the EFB-PF system, the EFB-RS system exhibited a lower accumulation of NO2−-N concentration.