An analysis of composite samples of 820 lake trout, walleye, steelhead, Chinook, and coho from the Laurentian Great Lakes reveals differences in contaminant processing among and between lakes which results in differing concentrations of bioaccumulative contaminants. Generally, contaminants are most concentrated in fish from Lake Michigan and least concentrated in fish from Lake Superior, with the notable exceptions of toxaphene and alpha-HCH. Differences in contamination patterns, however, are apparent not only among the lakes but between sites within a lake or even fish within a site. Lake trout composites from Lake Superior show an increase in the degree of chlorination of PCBs with increasing total PCBs. The PCB congener profile of lake trout from the Sturgeon Bay site of Lake Michigan is substantially different from that of the Saugatuck site of Lake Michigan, possibly due to the influence of contamination from nearby Green Bay. Finally, the ratios of selected PBDE and PCB congeners are much different in Lake Superior fish compared to fishes from all the other lakes. We hypothesize that this is a result of the colder temperatures and associated lower plankton growth rates in Lake Superior allowing PCB and PBDE uptake by phytoplankton to reach near equilibrium, thus enhancing the relative concentrations, in phytoplankton and the food web in general, of congeners that may be kinetically limited in other lakes.