Some urban estuaries on the west coast of the US are important habitats for several species of juvenile salmon and receive multiple stresses from human activities. Because these estuaries often receive multiple inputs of anthropogenic chemicals there is cause for concern that juvenile salmon migrating through polluted waterways may take up toxic chemicals which cause adverse biological effects. Accordingly, as part of an ongoing multiyear study in Puget Sound, WA, juvenile chinook salmon (Oncorhynchus tshawytscha) are being sampled from contaminated urban estuaries (Duwamish Waterway in Seattle and Commencement Bay in Tacoma), a non-urban estuary (Niisqually Estuary) and the respective hatcheries to determine exposure to chemicals, such as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and chlorinated pesticides that are suspected of eliciting chronic effects in fish. These compounds also serve as indicators of the myriad anthropogenic chemicals that are entering some coastal waters. Juvenile salmon from an urban and nonurban estuary were also held in the laboratory to determine if this contaminant exposure altered immune function or growth and survival. The findings of increased chemical contaminant exposure and reduced survival, impaired growth, and suppressed immune function suggest a potential for adverse health effects in juvenile salmon as they migrate through urban estuaries to a marine environment and that potential effects to the population may be significant. Although other urban-related perturbations of the estuarine habitat may be critically important to the health of salmon, such as reductions in normal water flows and loss of habitat to urban development, the impact of chemical contaminants on juvenile salmon must also be considered.