Juvenile salmon migrating from freshwater into Puget Sound en route to the Pacific Ocean encounter a wide range of water quality conditions that may impair their health, depending on their migration route and the duration of time spent in contaminated habitats. In 2013, we measured contaminant exposure in juvenile Chinook salmon from estuary, nearshore, and offshore habitats, including persistent organic pollutants (POPs) in whole-body fish samples, polycyclic aromatic hydrocarbons (PAHs) in stomach contents, and trace metals in gill tissues. Approximately one third of the Chinook salmon sampled from Puget Sound had elevated concentrations of toxic contaminants, high enough to affect their early marine survival. Levels of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in whole body samples of salmon from the Snohomish, Green/Duwamish and Hylebos/Puyallup estuary and nearshore habitats, and PCBs in fish from the offshore habitat of the Whidbey and Central Basins were high enough to potentially cause adverse effects, including reduction in growth, disease resistance, and altered hormone and protein levels. Additionally, levels of PAHs in stomach contents of salmon from the Snohomish and Green/Duwamish nearshore habitats were high enough to potentially affect growth and alter plasma chemistry and lipid class profiles. Elevated concentrations of copper and lead were measured in gills tissue of salmon from developed nearshore habitats, however, the potential effects on salmon health are unknown. Results from this study and future monitoring will identify areas where salmon may be at risk of contaminant exposure so appropriate toxics reduction activities can be implemented and will track the effectiveness of recovery actions to improve the health of Puget Sound Chinook salmon