Alteration of natural flow patterns in rivers can modify energy pathways and patterns of micronutrient transfer between trophic levels. As we seek to restore elements of natural flow regimes to rivers an improved understanding of micronutrient retention and integration between trophic levels is required. Fatty acids are used in food web studies to assess food quality and to discriminate food resources and patterns of energy flow between trophic levels due to their constrained metabolic biosynthesis by animals. However, their utility may be confounded by selective retention or modification of dietary fatty acids by consumers. Cherax destructor, (the common yabby or crayfish) is an abundant and widespread mesoconsumer that links basal resources to apex predators. Despite the crayfish’s acknowledged importance to aquatic food webs, crayfish biosynthesis of fatty acids and variation of their fatty acid profiles between habitats is poorly understood. We conducted a 70 day feeding trial to compare growth and survival of crayfish fed three contrasting diets – a poor quality detritus-based diet, a high protein invertebrate diet and a high quality commercial aquaculture pellet. Fatty acid profiles were obtained for each dietary treatment and contrasted with crayfish fatty acid profiles at the end of the experiment. We also collected wild crayfish from floodplain wetland and river habitats and obtained fatty acid profiles from their stomach contents and body tissue to compare with experimental crayfish. Experimental crayfish fed high quality commercial pellets doubled in mass during the 70- day assay, invertebrate fed crayfish growth was intermediate and growth of crayfish fed detritus was negligible. Fatty acid profiles of crayfish fed different foods were distinct from each other and from the fatty acid profiles of their diets. Proportions of the polyunsaturated omega–6 fatty acid linoleic acid (LIN, 18:2n6) in crayfish followed the same inequality observed in growth and diets – pellets > invertebrates > detritus. Pellet fed crayfish preferentially assimilated greater proportions of fatty acids 20:4n-6 (ARA), 20:5n-3 (EPA) 18:1n-9 (OA) and 16:1n-7 (POA) into their tissue. Fatty acid profiles of floodplain crayfish differed to profiles of riverine crayfish and floodplain crayfish had higher concentrations of essential fatty acids ARA and LIN in their tissues. Fatty acid biosynthesis by crayfish was best described by a fatty acid allostasis hypothesis rather than homeostasis – whereby fatty acid profiles of crayfish were shaped by their diet, and selective integration and modification of high quality fatty acids from basal resources rich in these micro–nutrients led to higher concentrations in crayfish tissues. Floodplain habitats are known to provide higher quality basal food resources for mesoconsumers than riverine habitats, and here we identify one mechanism by which that may be extended to subsequent trophic levels.