Abstract: To study the effects of benthic algae on the phosphorus (P) fractions in the submerged soils in water-level-fluctuating zone of the Three Gorges Reservoir (TGR), simulated experiments were conducted under indoor conditions. The results indicated that benthic algae utilized more AI-P compared with other forms of P, and the growth of the algal was inversely related to the AI-P content that the Al-P content decreased when the conditions were suitable for algal growth. Moreover, benthic algae variously affected the iron-phosphorus (Fe-P) in different layer of soil. Benthic algae had the greatest effects on Fe-P on 2-4 cm layer. In addition, the contents of O-P and Ca-P in different soil depths showed no significantly changes. In the late period of this experiment, the contents of Fe-P, O-P and Ca-P all showed a declining trend whereas Al-P showed a sign of increasing. Impoundment of TGR and benthic algae biofilm significantly increased P availability in the submerged soil and enhanced the transformation of inorganic-P into more soluble fractions.