A field study was conducted to examine bioaccumulation of polychlorinated biphenyls (PCBs) for hatchery-raised and naturally reared (wild) ocean-type juvenile chinook salmon outmigrating through the Lower Duwamish Waterway (LDW), a contaminated urban estuary in Seattle, WA, USA. These results show differences in bioaccumulation of PCBs over time and space in this estuary, which may also occur for any contaminant that is distributed heterogeneously in this system. Highly mobile, outmigrating salmon accumulated approximately 3-5 times more PCBs on the east side of the LDW than fish on the west side, which is supported by an almost identical difference in mean sediment concentrations. The tPCB concentration data suggest that for most of the spring and early summer, juvenile chinook were likely segregated between the east and west side of the LDW, but may have crossed the channel later in the year as larger fish. Additionally, we used biota-sediment accumulation factors to assess the relative degree of bioaccumulation and explore these factors as potential metrics for predicting adverse sediment concentrations. These results highlight the importance of time and space in sampling design for a highly mobile species in a heterogeneous estuary.