Hatchery programs have been used as a conservation tool to bolster declining populations of Chinook Salmon Oncorhynchus tshawytscha along much of the North American Pacific coast. In many watersheds, hatchery stocks are released concurrently with the wild population, thus raising the potential for density‐dependent effects. Competition for prey resources during the critical period for early marine growth and survival may diminish the foraging capacity and growth potential of wild Chinook Salmon, highlighting the importance of a diverse and productive delta habitat mosaic. We used an integrated diet approach with stomach content and stable isotope analyses to evaluate contrasting patterns of habitat use and prey consumption in a fall‐run population of juvenile Chinook Salmon from the Nisqually River delta in Puget Sound, Washington. We examined size‐class and origin‐level differences throughout a gradient of delta habitat types. Wild (unmarked) and hatchery juveniles exhibited distinct habitat use patterns whereby unmarked fish were captured more frequently in tidally influenced freshwater and mesohaline emergent marsh areas, while hatchery fish were caught more often in the nearshore intertidal zone. Consequently, hatchery fish were less likely to consume the energy‐dense terrestrial insects that were more common in freshwater and brackish marshes. Stable isotope signatures from muscle and liver tissues corroborated this finding, showing that unmarked juveniles had derived 24–31% of their diets from terrestrially sourced prey, while terrestrial insects only made up 2–8% of hatchery fish diets. This may explain why unmarked fish were in better condition than hatchery fish and had stomach contents that were 15% more energy‐rich than those of hatchery fish. We did not observe strong evidence for trophic overlap in juvenile Chinook Salmon of different rearing origins, but our results suggest that hatchery juveniles could be more sensitive to diet‐mediated effects on growth and survival.