Long- and short-term levels and trends of polychlorinated biphenyls (PCBs) in lake trout (Salvelinus namaycush) and walleye (Sander vitreus) from the Canadian waters of the Great Lakes are examined using the bootstrap resampling method in light of the Great Lakes Strategy 2002 (GLS-2002) objective of decrease in concentrations by 25% during 2000–2007. This objective has been set as an indicator of progress toward the long-term goal of all Great Lakes fish being safe to eat without restriction. Lake Superior lake trout and walleye PCB concentrations were almost unchanged between 1990–2006, and the bootstrap analysis suggests that the probability of achieving the GLS-2002 objective is negligible (< 2%). The PCB levels in Lake Huron lake trout and walleye are decreasing; the declines between 2000–2007 are estimated to be 25–35% and 5–30%, respectively. In contrast, Lake Erie walleye concentrations will likely increase by 25–50% between 2000–2007. For Lake Ontario lake trout, achieving the 25% reduction target seems highly probable with a likely decrease of 45–55%; for Lake Ontario walleye, the probability of achieving such a reduction is only 8% with an expected change of −13 to 15%. Although the targeted reduction may not be achieved for walleye from Lakes Superior, Huron, and Ontario, their best projected 2007 PCB levels are below the unlimited fish consumption guideline of 105 ng/g wet weight used by the Ontario Ministry of the Environment. In contrast, although there are high probabilities of achieving the goal for lake trout from Lakes Huron and Ontario, their best projected 2007 PCB levels (160 and 370 ng/g ww, respectively) will continue to result in consumption restrictions. Lake Superior lake trout concentrations may remain unchanged at the current elevated level of 160 ng/g ww. For Lake Erie fish, the projected 2007 concentrations and the increasing trends are both worrisome. Additional measurements beyond 2007 are necessary to confirm these estimates because of the observed periodic oscillations in the concentrations.