Study was made on the use of hydroponic bio-filter method (HBFM) for eutrophic surface water. Results show that HBFM can remove 16.8% of TN and 30.8% of TP at the hydraulic loading rate (HLR) of 3.0 m3/(m2 x d). The removal loading rate of TN and TP can accordingly reach 1.0 and 0.1 g/(m2 x d) respectively. The sedimentation of particulate nitrogen and particulate phosphorus plays a major role in nitrogen and phosphorus removal, and its contribution is 62.2% and 75.9% respectively. The optimal HLR of HBFM ranges from 3.0 to 4.0 m3/(m x d). The intension of secateur for Nasturtium officinale has some effect on its uptake rate, thus the length of cut when harvesting should be less than 10 cm. The harvesting frequency of once a month for Nasturtium officinale has no effect on nitrogen and phosphorus removal of HBFM.