As feed-additive aquaculture expands to open ocean areas, there is concern that ecologically important habitats may be adversely impacted by sedimentation of farm wastes. In this study, we investigated assimilation of salmon faecal wastes by an ecosystem engineering bivalve that occurs in open ocean environments (Atrina zelandica), as well as effects on physiology and fatty acid metabolism. A. zelandica were subjected to one of 3 treatment diets (fish faeces, 1:1 mix of algae:faeces and algae) in a 51 d laboratory trial. We found a diet-related response in fatty acid composition, including increased prevalence of oleic acid (OA) in digestive tissues of A. zelandica fed on both the fish faeces diet and the mixed diet, indicating fish wastes were assimilated in both treatments. Fish waste consumption was related to a more marked reduction in fatty acid content of digestive gland, as well as lower proportions of long-chain polyunsaturated fatty acids (LC-PUFA) in digestive tissues. Fatty acid composition in gonad and muscle tissues was more strongly influenced by sex. Regardless of dietary treatment, females accumulated C18 fatty acids in gonad tissues, particularly OA, which may preclude the use of OA as a fish waste tracer in this organ. The accumulation of specific fatty acids according to sex may indicate a capacity for preferential selection and retention or biosynthesis of biologically important fatty acids. If present, these mechanisms may increase resilience of A. zelandica to stress from deficiencies in LC-PUFA when using fish wastes as a trophic subsidy.