Suspension‐feeding bivalves play an important role in coastal ecosystems by affecting near‐bed hydrodynamics and, subsequently, rates of biodeposition. We designed a high‐resolution field study to investigate rates of sedimentation and biodeposition around individuals within beds of the large pinnid bivalve, Atrina zelandica, and to link these rates with sediment biogeochemical characteristics and macrofaunal community structure. The study was conducted at three sites arrayed along a gradient of increasing suspended seston concentration, enabling us to assess changes in the strength of the Atrina‐macrofauna interaction with background sedimentation. Sedimentation rates and inputs of organic carbon and nitrogen were higher close to individual Atrina (<=10 cm) compared to further away (>30 cm). Seafloor sediments nearer Atrina were enriched in carbon and nitrogen and had more diverse and abundant macrofaunal assemblages. The strength of this interaction decreased with increasing background sedimentation. Although other mechanisms, both biotic and abiotic, may explain some of these patterns, we have identified variations in macrofaunal community structure that at least partly can be linked to site‐specific sedimentation, at the small scale of single Atrina, nested within the larger landscape scale of Atrina beds, emphasizing Atrina's role in habitat modification, both structurally and functionally.