Presence of coastal aquaculture activities in marine landscapes is growing with impacts on the wild fish that share these habitats. However, it is difficult to disentangle subsequent ecological interactions between these activities and marine fish communities. We evaluated the impact of both salmon and halibut farms on mackerel (Scomber scombrus) and whiting (Merlangius merlangus) sampled near sea cages using condition indices and fatty acid (FA) biomarkers. Results of the stomach content analysis indicated that mackerel and whiting consumed waste feed which was also reflected in their modified FA profiles. Both mackerel and whiting had elevated levels of FAs that are of vegetable oils origin. The use of vegetable oils as replacement for marine oils is a lot more common in salmon farming than halibut farming. Additionally, the overall effects of the two fish farms were more pronounced in whiting than in mackerel sampled near the sea cages. By allowing discrimination between sources of trophic interactions, this method could lead to more informed decisions in managing different farming activities.