We performed dynamic linear modeling analysis on fish contaminant data collected from the Ontario Ministry of the Environment and Environment Canada to examine long-term trends of total mercury (THg) and polychlorinated biphenyls (PCBs) in Lake Erie. Several sport fish species (walleye, smallmouth bass, rainbow trout) with differences in their diet habits, food competition strategies and foraging patterns are characterized by weakly increasing trends of their THg levels in Lake Erie after the mid- or late 1990s. Similarly, our analysis shows that the decline rates of the PCB body burdens in white bass, smallmouth bass, freshwater drum and whitefish have slowed down or have switched to weakly increasing rates over the last decade. Our analysis also provides evidence that the rainbow trout and coho salmon PCB concentrations have been decreasing steadily but the associated rates were fairly weak. The systematic shifts in energy trophodynamics along with the food web alterations induced from the introduction of non-native species, the new role of the sediments as a net contaminant source, and the potentially significant fluxes from the atmosphere stand out as some of the hypotheses proposed to explain the limited Lake Erie response in recent years to the various contamination mitigation strategies.