In southern China, the increasing nutrient loading coupled with year-round warm weather in water sources promotes the growth of cyanobacteria, which can produce cyanotoxins, especially the potent liver toxins called microcystins (MCs). In order to purify raw water in a cost-efficient and environmentally friendly way, an ecological floating bed (EFB) experiment had been conducted to verify the viability. The removal efficiencies of total microcystin-LR (TMC-LR) averaged 42.4, 48.5, 43.0, and 36.3% at flow rates of 0.5, 2.0, 4.0, and 10.0cm/s, respectively. Different flow rates had no significant effect on microcystin-LR (MC-LR) absorption by plant, and the uptake in Oenanthe javanica was root over leafage. The protozoa and metazoan were different in amounts observed in the rhizosphere from EFB at different flow rates. Investigations of the potential for biodegradation of MC-LR had been carried out through well-controlled microcosm using EFB sediment as inocula. MC-LR could be degraded aerobically from 2mg/L to below the detection limit at 25 degrees C in 5d with a lag phase of 2d by EFB sediment at flow rate of 2.0cm/s. Taking the hydraulic and treatment efficiencies into consideration, the flow rate of 2.0cm/s was recommended for site selection. And these findings suggested that the flow rate affected the zooplankton grazing and bacteria degradation more than plant absorption of MCs. In addition, it was observed that TMC-LR removal efficiency showed positive linear correlation with the removal efficiencies of total phosphorus, chemical oxygen demand, and chlorophyll-a, respectively.