Oysters and seagrasses provide structurally complex estuarine habitat for fish and invertebrate species. On the U.S. West Coast, complex oyster habitat was historically provided by the native Olympia oyster Ostrea lurida but is now provided by the commercially cultured oyster Crassostrea gigas. Ostrea lurida is found in subtidal and low intertidal areas, whereas C. gigas is predominantly cultured at higher intertidal elevations, resulting in a potential shift in available habitat for other fish and invertebrates that use this intertidal habitat. This change in the available habitat and its use was examined for the juvenile Dungeness crab Metacarcinus magister, and results showed the following: (1) comparable crab densities in remnant and restored populations of O. lurida and cultured C. gigas in two estuaries, (2) generally higher crab densities in both of these shell habitats than those observed in eelgrass Zostera marina or open mud habitat, (3) contemporary juvenile crab density in intertidal areas of Willapa Bay was most influenced by distance from the estuary mouth (declining with increasing distance) but also declined with increasing tidal elevation, and (4) when extrapolated to the estuarine ecosystem scale using areal estimates of habitat coverage, historical habitat provided by O. lurida potentially produced three times more juvenile crabs than those currently produced in cultured C. gigas. Nonetheless, both intertidal oyster habitats contribute more to juvenile crab production than eelgrass or open unstructured mud, and the ecosystem services associated with the placement of native and commercial oyster beds should be considered when defining goals for and permitting both aquaculture and native oyster restoration in Willapa Bay and other U.S. West Coast estuaries. Managers should consider this shifting temporal baseline in intertidal habitat provision, but also conducting similar evaluations at this broader estuary scale when evaluating habitat value for other resources that use these habitats differently.