The bioaccumulation and biotransformation of toxaphene was examined in the food webs of Lake Superior and Siskiwit Lake (Isle Royale) using congener specific analysis as well as stable isotope ratios of carbon and nitrogen to characterize food webs. Toxaphene concentrations (calculated using technical toxaphene) in lake trout (Salvelinus namaycush) from the western basin of Lake Superior (N = 95) averaged (±SD) 889 ± 896 ng/g wet wt and 60 ± 34 ng/g wet wt in Siskiwit Lake. Major congeners in lake trout were B8-789 (P38), B8-2226 (P44), B9-1679 (P50), and B9-1025 (P62). Toxaphene concentrations were found to vary seasonally, especially in lower food web organisms in Lake Superior and to a lesser extent in Siskiwit Lake. Toxaphene concentrations declined significantly in lake herring (Coregonus artedii), rainbow smelt (Omerus mordax), and slimy sculpin (Cottus cognatus) as well as in zooplankton (> 102 &mn;m) and Mysis (Mysis relicta) between May and October. The seasonal variation may reflect seasonal shifts in the species abundance within the zooplankton community. Trophic magnification factors (TMF) derived from regressions of toxaphene congener concentrations versus δ¹⁵N were > 1 for most octa- and nonachlorobornanes in Lake Superior except B8-1413 (P26) and B9-715. Log bioaccumulation factors (BAFs) for toxaphene congeners in lake trout (ng/g lipid/ng/L dissolved) ranged from 4.54 to 9.7 and were significantly correlated with log octanol-water partition coefficients. TMFs observed for total toxaphene and congener B9-1679 in Lake Superior were similar to those in Arctic lakes, as well as to previous studies in the Great Lakes, which suggests that the bioaccumulation behavior of toxaphene is similar in pelagic food webs of large, cold water systems. However, toxaphene concentrations were lower in lake trout from Siskiwit Lake and lakes in northwestern Ontario than in Lake Superior possibly because of shorter food chains and greater reliance on zooplankton or other pelagic invertebrates.