An 18-year record of stable isotopes from Atlantic salmon (Salmo salar) migrating to two different regions of the North Atlantic reveals climate-driven subdecadal variations. Time-series of carbon isotopes in one salmon stock, thought to feed in the Faroes/ Iceland Basin area, show Subpolar Gyre (SPG) modal variability, which is not seen in fish feeding in the Norwegian Sea. At times of weak SPG circulation, when waters in the Iceland Basin are relatively warm, carbon isotope values are somewhat negative, suggesting possible changes in phytoplankton community structure. The fluctuations in plankton community dynamics suggested by the stable isotope values are coincident with fluctuations in the estimates of marine mortality in one sea-winter fish feeding in the Norwegian Sea, but not in those feeding in the Iceland Basin. Marine mortality in salmon feeding in the Iceland Basin is therefore likely to be more strongly influenced by factors other than bottom-up control. Time-series analysis of stable isotopes in consumer tissues provides information on the interaction between climate and ecosystem dynamics on the scale of individual stocks and cohorts.