We investigated the habitat use and size structure of the fan mussel, Pinna nobilis L. in the Alfacs Bay (Ebro Delta, Spain, NW Mediterranean). Shore-parallel transects were conducted to assess the abundance, size, and orientation of individuals and to record habitat features along the Banya Sandspit, at depths of 20 to 130 cm. Results showed two distinctive areas in terms of population density, marked by the end of local salt pan dikes that we named Good Habitat (GH) and Bad Habitat (BH). To extrapolate these results to the full area of BH and GH, perpendicular transects were conducted to determine the local bathymetry. Then, the underestimation of individuals due to the effects of distance, depth and seagrass cover (Distance 6 computer package) was added to raw abundances to obtain a corrected population of 90303 individuals (12085 in the BH and 782018 in the GH), the largest so far reported at such low depths. Most recorded individuals were adults (40 to 60 cm shell length), with no occurrence of sizes <20 cm, and with a strong association with Cymodocea nodosa seagrass beds. Given the shallow distribution of the population, the absence of small sizes during the study period, and the presence of human activities that may damage P. nobilis and its habitat, the development of a management plan appears imperative for the conservation of the species.