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Duckweed (Lemnaceae) can support the development of freshwater aquaculture if used as extractive species in Integrated MultiTrophic Aquaculture (IMTA) systems. These aquatic plants have the advantage of producing protein-rich biomass that has several potential uses. On the contrary, other biological compartments, such as microalgae and bacteria, present in the water and competing with duckweed for light and nutrients cannot be harvested easily from the water. Moreover, as phytoplankton cannot easily be harvested, nutrients are eventually re-released; hence, this compartment does not contribute to the overall water remediation process. In the present study, a mesocosm experiment was designed to quantify the portion of nutrients effectively removed by duckweed in a duckweed-based aquaculture wastewater remediation system. Three tanks were buried next to a pilot-scale IMTA system used for the production of rainbow trout and perch. The tanks received aquaculture effluents from the adjacent system, and 50% of their surface was covered by duckweed. Daily water analyses of samples at the inlet and outlet of the mesocosm allowed quantification of the amount of nutrients removed in total. The portion removed by duckweed was determined by examining the nutrient content in the initial and final biomass. The portion of nutrients removed by other compartments was similarly estimated. The results show that duckweed is responsible for the removal of 31% and 29% of N and P, respectively. Phytoplankton removed 33% and 38% of N and P, respectively, while the biofilm played no major role in nutrient removal. The remainder of the removed nutrients were probably assimilated by bacteria or sedimented. It is speculated that a higher initial duckweed density can limit phytoplankton growth and, therefore, increase the portion of nutrients removed by the duckweed compartment.