In this study, a fatty acid dilution model was coupled with a dynamic nutrient demand model to provide an integrated model capable of predicting the whole-body and fillet lipid and fatty acid levels of Atlantic salmon (Salmo salar) following a change in dietary fatty acid profile. Based on knowledge of the initial fish and dietary fatty acid compositions, diet digestible energy density, the water temperature and duration of feeding, the model demonstrated that it was possible to predict a range of parameters, including the growth, feed utilisation, whole-body and fillet (Norwegian Quality Cut; NQC) total lipid, and fatty acid levels of the fish. The model was validated against five separate experiments, including two farm-based trials with harvest size fish. Validation experiments involved fish ranging in size (initial weights to final weights) from 138 g/fish to 5138 g/fish and running for durations of between 66 and 323 days. For the laboratory experiments, prediction of growth, feed utilisation and fatty acid deposition proved to be highly predictable (R2 > 0.998). Fatty acid profiles from both short and long-term cage trials were also highly predictable. Despite the reduced level of weight change in the short-term cage trial, and the higher variability that was observed in growth performance, the fatty acid deposition still showed high levels of correlation (R2 > 0.996), between the modelled and measured fatty acid levels in the fish fillet. Departure from linearity was more evident in the long-term cage trial, but correlation still exceeded R2 > 0.995 for all treatments. Prediction of whole-body and NQC total lipid levels was less accurate, with correlations being R2 = 0.962 and R2 = 0.909 respectively. Model outputs were generally more accurate with greater weight change and/or experiment duration. The outcome of this study shows that the model developed here provides a useful tool for the estimation of the fatty acid composition of Atlantic salmon following a change in dietary fatty acid composition. This could help assist in the more judicious use of dietary long-chain omega-3 fatty acids for commercial salmon farming.