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An aquaponics system (AS) is an integrated system that combines a recirculating aquaculture system and a hydroponics system (HS). It is designed to recover nutrients released from fish and transfer them to plants to provide a system more environmentally-friendly than the two systems working separately. As a result, several AS are under development, but little information is available about their overall performances. The aim of this study was to assess nutrient-use efficiency and environmental impacts of an AS, specifically a common carp-lettuce AS located in a greenhouse. Nutrient budgets of nitrogen (N) and phosphorus (P) were calculated and Life Cycle Assessment (LCA) was performed for the AS and for a lettuce Individual Hydroponics System (IHS), similar to the HS of the AS, operating in the greenhouse at the same time. The experiment was performed over a 52-day cycle, which corresponds to the growing time required to harvest marketable lettuce. The nutrient budgets were well balanced, with 24.6% of the N unaccounted-for, most likely due to N2 gas emission, and 6.6% of the P unaccounted-for, most likely due to having underestimated the quantity of sediment. At the beginning of the experiment, N represented 55.9%, 37.1% and 0.1% of the total N input in the formulated feed, stocked fish and lettuce seedlings, respectively. At the end of the experiment, N represented 47.6% and 0.4% of the total N input in the harvested fish and lettuce, respectively. At the beginning of the experiment, P represented 56.94%, 40.20% and 0.03% of the total P input in the formulated feed, stocked fish and lettuce seedlings, respectively. At the end of the experiment, P represented 51.52% and 0.42% of the total P input in the harvested fish and lettuce, respectively. LCA clearly indicated two environmental impact hotspots: the origin of nutrients and energy use. One kg of lettuce growth in the AS clearly had lower environmental impacts than that in the IHS for climate change, acidification, eutrophication, land competition and cumulative energy demand; however, a decrease in water dependence was not observed. The indicator for net primary production use highlighted the dependence of the AS on natural resources, especially fish meal and fish oil. Compared to the use of chemical nutrients in the IHS, the use of nutrients from formulated feed in the AS decreased climate change impact but increased the use of natural resources.