The Hudson River estuary has enormous spatial variation in polychlorinated biphenyl (PCB) contamination due in large part to historical point source discharges above Troy Dam. The Delaware River estuary has accumulated significant levels of PCBs through decades of industrial, municipal, and non-point source inputs. The overall goal of this research was to use existing data sets to compare and contrast the patterns of accumulated PCB congeners in sub-populations of American eels and striped bass inhabiting these two estuaries and surrounding coastal waters. Using principal component analysis and analysis of covariance (ANCOVA), inter- and intra-estuarine differences in accumulated congeneric patterns were denoted for both species. Results from our study support the idea that migratory behaviors of striped bass hamper the use of accumulated congener-specific PCB patterns in providing information on localized contamination, although major regional differences were seen between upriver Hudson River fish, downriver Hudson River fish and fish from other areas within this study. This study provides additional evidence for the use of the American eel as a biomonitoring tool, since its limited home range provides finer resolution of regional contamination.