Structured estuarine habitats, such as salt marshes, seagrass beds, and oyster reefs, are recognized as critical nurseries for juvenile fish and crustaceans. Estuarine habitat usage by fish, including juvenile Pacific salmon Oncorhynchus spp., was characterized by sampling with a modified tow net in Willapa Bay, Washington, where 20% of the intertidal area is utilized for shellfish aquaculture and thus is difficult to sample with conventional gear. Our goal was to compare fish use of relatively undisturbed habitats (open mudflat, seagrass, and channel habitats) with the use of nearby oyster culture habitat. Although many species showed significant temporal and spatial trends within the estuary, only Shiner Perch Cymatogaster aggregata exhibited a significant association with habitat. Juveniles of three salmonid species exhibited few associations with the low intertidal habitats over which they were captured or in the prey types they consumed there. Chinook Salmon O. tshawytscha, likely hatchery-released oceantype fish, were the most common salmonid captured, and they utilized low intertidal areas throughout the summer as their mean size increased from 85 to 100 mm FL. Diets consumed by these larger juvenile Chinook Salmon were not associated with benthic habitat but instead consisted primarily of (1) insects from nearby marsh or terrestrial habitats and (2) planktonic prey, like decapod larvae and tunicate larvaceans. Juvenile Coho Salmon O. kisutch and Chum Salmon O. keta were captured earlier (April and May) and fed on a slightly different suite of prey taxa, which were also primarily pelagic rather than associated with the intertidal benthos. Our findings suggest that in this relatively shallow coastal estuary, the role of benthic habitat is not closely linked to its value as a source of food for large juvenile salmon out-migrants utilizing the low intertidal areas where aquaculture occurs.Estuaries support a high diversity and density of fish and invertebrates (Beck et al. 2003;Gillanders et al. 2003;Able 2005). Within estuaries, structured habitats (e.g., marshes, seagrass, and other submerged aquatic vegetation [SAV]) provide trophic resources and refuge from predators, thus allowing small fish and invertebrates to reach greater density and diversity relative to those in unstructured habitats (e.g., open mudflat; Deegan et al.