Juvenile salmon exhibit high growth rates upon their arrival into the marine environment. Dietary changes from freshwater and estuarine habitats to those derived from the marine environment may play an important role in ultimate adult survival. We measured the total lipid and fatty acid (FA) composition of juvenile Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), and 18 of their potential prey items sampled from coastal waters during their first few months at sea. Coho salmon had significant reductions in their lipid content (% wet weight) between May and June, likely due to early marine growth. We did not find a significant drop between May and June Chinook salmon lipid content, which may indicate an earlier ontogenetic selection to marine prey that are higher in lipids and essential fatty acids (EFAs). Juvenile salmon ate prey of both high and low lipids. Significant FA compositional changes occurred for both coho and Chinook salmon between May and June. In May, the FA profile of juvenile salmon, especially coho salmon, did not resemble their prey items; however, in June, there was a strong correlation between salmon and their common fish prey as determined by gut content analysis. Significant increases in the level of EFAs, especially docosahexaenoic acid (DHA, 22:6n-3) accounted for the majority of the monthly differences in salmon tissue FA composition. In order for juvenile salmon to adequately meet their physiological requirements, they may have adapted to select advantageous prey with higher levels of EFAs, especially DHA, in order to rapidly increase their growth and ultimate survival.