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Polychlorinated biphenyl (PCB) congener concentrations measured in 1,189 sediment samples from Green Bay (MI/WI, USA), Lake Michigan (MI/WI, USA), and the Fox River (WI, USA) were analyzed statistically to evaluate whether PCB congener profiles in outer Green Bay are more similar to those observed in inner Green Bay or Lake Michigan. Similarities among PCB profiles were assessed with complementary multivariate analysis techniques: Principal component analysis (PCA), cluster analysis, and classification trees. The PCA indicated that profiles in outer Green Bay are distinct from those of inner Green Bay or Lake Michigan but are more similar to those of inner Green Bay. The outer bay profiles are dissimilar to profiles that would result from a simple process of mixing contaminated sediments from the inner bay with Lake Michigan sediments and, therefore, support the conclusion that contaminants in outer Green Bay come from discharges of the Fox River. Several classification trees based on small sets of congener proportions defined simple rules that consistently distinguished the regional profiles. Application of these rules to classify the outer bay samples suggests that the profiles of less than 7% of outer bay samples are similar to Lake Michigan profiles. These results are interpreted with respect to physical transport and chemical weathering processes that may account for the observed differences.