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Aquaculture policies that decrease the reliance on wild-caught fish and promote integrated multi-trophic aquaculture (IMTA) both aim to lessen the environmental footprint but often overlook economic-environmental trade-offs and neglect social, health, and broad-scale sustainability considerations. Here we present a new bio-physical model (FYNE) that bridges some of these gaps, by linking farm operational choices, such as feed choices and farm siting, with the nutritional value of the farm-gate seafood products and the resulting environmental eutrophication footprint at the farm level. The FYNE model operates both in conditions of monoculture or of IMTA production, and estimates feed composition effects on growth and omega-3 fatty acid content of Atlantic salmon (Salmo salar) and blue mussel (Mytilus edulis) , and nitrogen and carbon concentrations, the latter being a measure of the environmental eutrophication footprint of the farm. The model here developed integrates for the first time (i) an ecosystem model of an IMTA and (ii) a fatty acid dynamics model, with new models for salmon feed digestibility and mussel ingestion. The outputs span (i) production analysis for simulation of biomass; (ii) farm mass-balance analysis on deposition analysis and environmental eutrophication footprint; and (iii) product nutritional quality, in terms of fatty acid content. An application of the model to an IMTA farm in Scotland (UK) demonstrates how fatty acid and environmental changes can be modelled in tandem and could be used to support the industry to optimize the nutritional value of cultured species and manage aquatic environmental eutrophication footprint at farm level, informing feed and siting decisions. The model effectively predicts changes in omega-3 fatty acids, particularly DHA and EPA, in response to variations in feed composition. Notably, our results confirm that salmon waste has limited influence on mussel growth due to the spatial separation within the IMTA system, which emphasizes the need for strategic siting to enhance system productivity through effective waste recycling. Additionally, results show that while increasing fishmeal in diets enhances environmental outcomes, it reduces levels of critical fatty acids like DHA and EPA, underscoring the need for balanced feed formulations. The method developed in this study described a novel integrated model (FYNE) that extend previous modelling work by incorporating the influence of farmed species feed composition on fatty acid dynamics as well as the farming environmental factors. • Salmon and mussel fatty acid dynamics linked to growth models and environment. • Models influence of feed on IMTA species nutritional quality and environment. • Model replicates the changes in salmon PUFA content relative to dietary PUFA content over a growth cycle. • Integration of PUFA models with IMTA ecosystem model. • Models the relationship between diet composition, fatty acid content, and environmental footprint. [ABSTRACT FROM AUTHOR]