The continental shelf ecosystem on the Eastern Scotian Shelf (ESS) has experienced drastic changes. Once common top predators are a small fraction of their historical abundance, and much of the current community structure is now dominated by pelagic fishes and invertebrates. Embedded within this food web, Atlantic cod and gray seal populations have recently exhibited nearly opposite trends. Since 1984, cod populations have decreased exponentially at a rate averaging 17% per year, whereas gray seals have continued to increase exponentially at a rate of 12%. We reexamined the impact of gray seals on Atlantic cod dynamics using more than 30 years of data on the population trends of cod and gray seals while incorporating new information on seal diet and seasonal distribution. The closure of the cod fishery over 10 years ago allowed for a better estimation of natural mortality rates. We quantified the impact of seals on ESS cod by (1) estimating trends in seal and cod abundance, (2) estimating the total energy needed for seal growth and maintenance from an energetics model, (3) using estimates of the percentage of cod in the total diet derived from quantitative fatty acid signature analysis (QFASA) and of the size‐specific selectivity of cod consumed (derived from otoliths collected from fecal samples), and (4) assuming a gray seal functional response. Uncertainties of the model estimates were calculated using the Hessian approximation of the variance–covariance matrix. Between 1993 and 2000, cod comprised, on average, <5% of a gray seal's diet. Our model shows that, since the closure of the fishery, gray seals have imposed a significant level of instantaneous mortality (0.21), and along with other unknown sources of natural mortality (0.62), are contributing to the failure of this cod stock to recover.