Since 2016, the Mediterranean fan mussel Pinna nobilis (L. 1758) has undergone severe Mass Mortality Events (MMEs) throughout its entire range, leading to a drastic decline of the species. However, for reasons not fully understood, some coastal transitional ecosystems still host large extant populations, acting as refugia for the species. Pinna nobilis plays a key ecological role by increasing habitat structural complexity and contributing to overall ecosystem functioning. In the present study, the ecosystem engineering role of the species in lagoon environments has been assessed through a multi-scale analysis of the spatial distribution and three-dimensional structure of relict fan mussel shell fields in the Venice Lagoon. Underwater Structure-from-Motion (SfM) photogrammetric surveys were performed in 2022 by snorkel divers at a subtidal flat 1.5 meters deep colonized by Pinna nobilis in the central lagoon of Venice. To acquire images, a multi-camera rig and specific protocols tailored for low-visibility conditions were applied. High-resolution (submillimeter) orthomosaics and Digital Elevation Models (DEMs) were produced. Based on the DEMs, we investigated how vertically emergent fan mussel shells, including both living and dead individuals, modify seabed roughness and near-bed hydrodynamics, shifting the seabed into a markedly higher stress regime even at moderate flow velocities, with implications for sediment mobilization, near-bed turbulence, and vertical biogeochemical fluxes. An extensive monitoring campaign carried out in 2024 at 40 stations in collaboration with the Veneto Region, within the framework of the Interreg IT-SI POSEIDONE project, allows for a first quantitative estimation of the broader ecological role of the species at the lagoon scale. The implications of dead shells persisting in an upright position for several years following MMEs are presented. The results are discussed in relation to future research and conservation perspectives for Pinna nobilis and other habitat-forming macroinvertebrates in coastal transitional ecosystems.