Phosphorus internal loading from the sediment of a surface aquatic system is considered to be the primary source of phosphorus responsible for eutrophication. In this study, we propose a possible solution to intercept phosphorus liberated from sediment to overlying water by a membranous nano-barrier (MNB) with tunable capacity. The equilibrium could be attained within 2 h when the MNB interacted with phosphate-containing water. The intercepting capacity was almost unaffected when the solution pH was varied from 4 to 10. The laboratory-scale trial showed that the MNB could positively intercept phosphorus liberated from sediment when the MNB covered the sediment, and the MNB was easy to replace once it became phosphate saturated, making its actual application feasible. Generally, the novel MNB can be considered to be a possible pathway for eutrophication control in shallow surface aquatic systems and scenic water.