The management, restoration, and conservation of estuarine habitats would benefit from knowledge of habitat-specific functions that reflect important ecosystem services. Secondary production may provide a comprehensive metric of food web support because it synthesizes contributions of local primary production, food subsidies from other habitats, and the protective influences of habitat structure. Despite widespread perceptions of how habitats compare in food web contribution, few methodologically comparable studies on secondary production across multiple estuarine habitats exist. At field sites in North Carolina, USA, annual secondary production was estimated for macrobenthic infaunal and epifaunal communities in salt marshes, seagrass meadows, oyster reefs, intertidal and subtidal flats, and on shoreline stabilization structures. Habitats with hard emergent or biogenic structure generally exhibited higher secondary production than habitats lacking structure. Oyster reef had the highest secondary production, ranging from 467.3 to 853.7 g ash free dry mass (AFDM) m?2 yr?1, while shoreline stabilization structures ranked high because of dense epifaunal communities. Estimates of secondary production suggest ranking of natural habitats as oyster reef > salt marsh > seagrass > intertidal flat and subtidal flat. Undesirable impacts of shoreline stabilization structures on adjacent habitats made their inclusion in this ranking of food web support by habitat difficult. The importance of suspension feeders on oyster reefs, shoreline stabilization structures, and in some marshes suggests that secondary production patterns are partly influenced by external subsidies facilitated by support from habitat structure. Consequently, estuarine rehabilitation should include structural habitat elements that will contribute to ecosystem production at higher trophic levels. Without such habitat restoration, the fate of estuaries in the USA affected by anthropogenic stressors may be loss of habitat diversity and prevalence of low-trophic-supporting habitats.