In order to study the effects of different root systems in different submerged macrophytes on the vertical distribution of phosphorus fractions in sediments, V. natans and H. verticillata were applied and phosphorus concentrations in overlying water and underneath sediments were investigated during the growth season. Results showed that the contents of total phosphorus (TP), inorganic phosphorus(IP) and NaOH-P fractions in sediments decreased vertically in different levels during both submerged macrophytic groups. Both submerged macrophytic groups reached their maximum decreased values at the depth of 4.5 cm, decreased by 58.91 and 36.46 mg/kg, respectively, comparing with the control. The maximum decreased values of IP in groups of V. natans and H. verticillata appeared at the depth of 6.0 and 3.0 cm, and they decreased by 85.41 and 57.41 mg/kg, respectively, comparing with the control. The results indicated that the submerged macrophyte V. natans has higher ability in lowering down phosphorus fractions than H. verticillata in sediments.