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The impacts of climate change are increasingly apparent in the physical oceanographic environment of the global ocean, with cascading effects through individual species to entire food webs. Despite their importance, these ecosystem effects can be challenging to quantify and track. One angle from which to analyse ecosystem linkages is via compound-specific stable isotope analysis of carbon and nitrogen focused on individual amino acids. These analyses can provide individual-level information (e.g., dietary sources, trophic position) as well as ecosystem-level information (e.g., variability in biogeochemical cycling at the base of the food web, nutrient regimes, food web structure). In this study, we analyzed C and N stable isotopes in archived scales of haddock (Melanogrammus aeglefinus) collected over almost a century from Georges Bank (northeast US) to investigate changes in the diet and trophic status of the haddock population driven by climate change. Specifically, we used nitrogen isotopes to identify secular changes in the input of warm slope waters to the Gulf of Maine over the time series. In contrast, carbon isotopes in essential amino acids suggest that there have been relatively small changes in the source of carbon fueling haddock biomass over the past 100 years and nitrogen isotopes indicate negligible changes in haddock trophic position despite major oceanographic and climatic changes over this time period. Overall, we demonstrate the application of cutting edge molecular isotope tools to a historical archive to examine food web architecture over time in a changing oceanographic environment.