Robust sustainability assessments of aquaculture systems require life cycle assessment (LCA) methodologies that go beyond carbon footprint alone to include indicators such as eutrophication potential, acidification potential, and land use, while also identifying possible environmental trade-offs. In Denmark, rainbow trout farming is carried out using three distinct production models, two of which incorporate nature-based biofiltration technologies , wood chip bioreactors and tree marshes , designed to mitigate nutrient emissions and support biodiversity. This study evaluates the environmental performance of these systems, with a particular focus on the effectiveness of biofiltration in reducing nitrogen emissions. Integrating wood chip bioreactors and tree marshes may reduce nitrogen emissions but evaluating the potential increases in other impact categories is also necessary. Following the principles of the EU Product Environmental Footprint (PEF) framework, we assess the impacts associated with producing 1 ton of live-weight trout at the farm gate. Special attention is given to denitrification modeling, where the carbon-to-nitrogen ratio in biofilters plays a critical role in determining the emission of nitrogen gas (N₂) versus nitrous oxide (N₂O), the latter of which has a global warming potential 265 times that of CO₂.