Free-floating aquatic plants are important invasive alien species whose excessive growth strongly affects freshwater ecosystems and their ecological service functions worldwide. Due to their rapid reproduction rate and the difficulty in their removal using common methods, the management of these aquatic weeds is still challenging. In this study, we proposed a strategy to control giant duckweed (Spirodela polyrhiza) in a highly eutrophic pond by blocking the supply of phosphorus by greatly lowering the phosphorus concentration in water using Zeofixer®, a novel lanthanum-containing P-inactivation agent. We found that the application of Zeofixer® satisfactorily eliminated the aquatic weed from the study pond. Zeofixer® had a high affinity for phosphate with a maximum adsorption capacity of 21.19 mgP/g, and it reduced the concentration of dissolved inorganic P, which was the major form of P species in the pond, from 1.60 to 0.005 mg/L. Amendment of pond sediment with Zeofixer® greatly diminished the P concentration in water under either oxic or anoxic conditions, although the latter caused a great release of P from sediment when compared with the former. After Zeofixer® treatment, the releasable P fractions in the sediment were substantially converted to stable P fractions, enabling the inactivation of P and the retardation of future P release. In conclusion, the free-floating aquatic plants in bodies of water could be thoroughly and permanently controlled using P-inactivation agents.