Polychlorinated naphthalenes (PCNs) were measured in lake trout and walleye over the period 2004-2018, utilizing isotope dilution techniques with high-resolution gas chromatography/high-resolution mass spectrometry to assess concentrations and toxic equivalence (TEQ). An age-trend model was applied to mitigate the effect of a changing lake trout age structure. Most Great Lakes Fish Monitoring and Surveillance Program sampling sites demonstrated significant half-life and percent decreases for lake trout total PCNs and total TEQ over the 2004-2018 period, the exceptions being Lake Erie lake trout and walleye which illustrated increasing concentrations. Great Lakes total PCN concentrations ranged between 5701 and 100 pg/g ww, whereas total PCN TEQ concentrations ranged between 8.89 and 0.13 pg-TEQ/g ww. Based on the average number of chlorines per naphthalene, we determined that the overall lake trout and walleye PCN congener distribution has significantly shifted to a lower-chlorinated composition in the Great Lakes (5.33 to 4.48 Cl/CN) and has resulted in a substantial 59.1% reduction of the overall total PCN TEQ burden. A prominent PCN concentration trend breakpoint was observed in Lake Ontario lake trout over the 2012-2016 period likely associated with hazardous waste cleanups, channel dredging, and spoils disposal in the Detroit River and western-basin of Lake Erie.