Lake trout Salvelinus namaycush were extirpated from Lake Ontario circa 1950 owing to commercial and recreational fishing, predation by sea lampreys Petromyzon marinus, and habitat degradation. Since the 1970s, substantial efforts have been devoted to reestablishing a self-sustaining population through stocking, sea lamprey control, and harvest reduction. Although a stocking-supported population has been established, only limited natural reproduction has been detected. Since the 1990s, surveys have indicated a continuing decline in overall abundance despite fairly static stocking levels. We constructed a statistical catch-at-age model to describe the dynamics of Lake Ontario lake trout from 1985 to 2007 and explore what factor(s) could be causing the declines in abundance. Model estimates indicated that abundance had declined by approximately 76% since 1985. The factor that appeared most responsible for this was an increase in age-1 natural mortality rates from approximately 0.9 to 2.5 between 1985 and 2002. The largest source of mortality for age-2 and older fish was sea lamprey predation, followed by natural and recreational fishing mortality. Exploitation was low, harvest levels being uncertain and categorized by length rather than age. Accurate predictions of fishery harvest and survey catch per unit effort were obtained despite low harvest levels by using atypical data (e.g., numbers stocked as an absolute measure of recruitment) and a flexible modeling approach. Flexible approaches such as this might allow similar assessments for a wide range of lightly exploited stocks. The mechanisms responsible for declining age-1 lake trout survival are unknown, but the declines were coincident with an increase in the proportion of stocked fish that were of the Seneca strain and a decrease in the overall stocking rate. It is possible that earlier studies suggesting that Seneca strain lake trout would be successful in Lake Ontario are no longer applicable given the large ecosystem changes that have occurred subsequent to invasion by dreissenid mussels.