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Our goal was to understand the mechanisms behind the impact of nutrient enrichment at intermediate distances from aquaculture on the interactions of a subtidal macroalgae community with its main grazer, the sea urchin <i>Paracentrotus lividus</i>. We assessed the diversity and cover of the macroalgal community, the abundance and biometrics of the sea urchins, the carbon and nitrogen elemental and isotopic compositions, and their metabolome in two stations, at an intermediate distance (station A) and away (station B) from a fish cage facility in the Aegean Sea (Greece), during the warm and cold seasons. The nutrient input at station A favored a shift to a macroalgal assemblage dominated by turf-forming species, depleted of native-erected species and with a higher abundance of invasive algae. A stable isotope analysis showed fish-farm-associated nitrogen enrichment of the macroalgae and trophic transfer to <i>P. lividus</i>. A decrease in metabolites related to grazing, reproduction, and energy reserves was found in <i>P. lividus</i> at station A. Furthermore, the metabolomic analysis was able to pinpoint stress in <i>P. lividus</i> at an intermediate distance from aquaculture. The chosen combination of traditional ecology with omics technology could be used to uncover not only the sublethal effects of nutrient loading but also the pathways for species interactions.