ABSTRACT: On the extensive tidal flats of Willapa Bay (Pacific coast, USA), oyster culture, seagrass and mudflat create a mosaic of intertidal habitats. Structured habitats are generally considered to increase abundance and diversity of associated species, but less attention has been paid to roles of different kinds of structure (seagrass meadows, reefs, farm infrastructure) or co-occurring structure in shaping nekton assemblage structure. Here, we investigate the effects of different oyster culture methods (suspended culture and bottom culture) on nekton communities and abundance across a gradient of seagrass habitats, during multiple seasons, and using both seine and video sampling methods. Of 23 major estuarine taxa, two generally associated with vertical structure (eelgrass or suspended culture), three were seagrass specialists, and three primarily used habitats lacking vertical structure (mudflat and bottom culture). Where oyster culture was present, five taxa associated with on-bottom and two taxa associated with suspended culture. Assemblage structure responded to co-occurring structure as expected from responses to each structure type independently (i.e. additive effects of seagrass and oyster culture). In contrast to much empirical evidence in structured habitats, seagrass density was a poor predictor of overall fish abundance. These findings together suggest that maintaining a mosaic of available habitats is favorable for promoting diversity in Willapa Bay.