Estuaries provide vital nursery habitat for threatened Chinook salmon (Oncorhynchus tshawytscha) by promoting an ecological portfolio effect, whereby multiple habitat types and environmental strata maximize foraging opportunities for out-migrating salmon by varying the abundance and composition of prey through space and time. To study this portfolio effect, we evaluated the foraging capacity of five estuarine habitat types within the Nisqually River Delta (Puget Sound, Washington, USA). Within each habitat, we sampled invertebrate prey resources from the terrestrial, aquatic, benthic, and epifaunal strata and compared them to juvenile salmon diets from corresponding sampling events. We found that the emergent salt marsh supplied twice as much aquatic prey biomass as any other habitat (720–5523 mg/m3), followed by the mudflat (246–2543 mg/m3) and eelgrass (Zostera marina; 141–2694 mg/m3) habitats. Despite some evidence for selectivity, juvenile salmon diets exhibited substantial compositional overlap, especially when compared to among-habitat differences in available prey resources. Fish that were captured in salt marsh, mudflat, and eelgrass consumed aquatic crustaceans such as mysids, while fish captured upriver in forested and transitional marshes ate a higher proportion of adult and larval insects. The availability and consumption of greater quantities of energy-poor crustaceans in the salt marsh and lower quantities of energy-rich insects upriver highlights a quantity-for-quality tradeoff among estuarine habitats. Our findings indicate that the timing, productivity, and diversity of prey across multiple habitat types and environmental strata determine an estuary’s capacity to support foraging for multiple life history strategies, size classes, and cohorts of juvenile salmon.