Physiological condition contributes to the productivity of anadromous salmonids and is particularly relevant in species that include large-scale migrations in their life histories. Sockeye salmon (Oncorhynchus nerka) cease feeding before beginning their spawning migration to freshwaters and rely solely on energy storage for physiological function and survival. A considerable amount of energy is derived from lipids and previous research has highlighted the nutritional value of the eicosapentaenoic acid and docosahexaenoic acid (omega-3 fatty acids) for human health. Additionally there is now a broad recognition that salmonids play an integral part in coastal food webs and provide substantial energetic resource subsidies to numerous consumers such as bears, birds, and resident fishes. What remains largely unknown about salmon lipid physiology is an understanding if a temporal selection for the metabolism of specific fatty acids exists, and if so then to what extent. Here, we characterized lipid (fatty acid) profiles across three major stages in freshwater migration (freshwater entry, midway, and senescence). Fatty acids were isolated by following a modified Bligh-Dyer protocol. We used gas chromatography and modeling functions to identify and quantify fatty acid trends. Total fatty acids were used as an indicator of available stored energy in tissues, while the relative quantities of individual fatty acids provide information on how these lipids are allocated to either energy for migration or specific physiological functions. Total fatty acids declined through the salmon run, but declines were not even across individual fatty acids. The proportion of several fatty acids (e.g. 24:1n-9) drastically decreased by senescence, while some fatty acid reserves were nearly completely metabolized (e.g. 18:3n-3). Our results have implications for understanding the mechanism and extent that migrating salmonids utilize lipids, which may partially determine their overall reproductive success.