Pinna nobilis Linnaeus, 1758 is a Mediterranean endemic bivalve critically endangered due to a severe epidemic caused mainly by the parasite Haplosporidium pinnae. Presently, live populations in Spanish waters are restricted to the Ebro Delta (Catalonia) and the Mar Menor (Murcia). The coastal lagoon of the Mar Menor has faced several eutrophication crises since 2016, which pose a threat to the survival of P. nobilis. Since 2016, >95% of the specimens of this species have died due to recurrent episodes of eutrophication in the lagoon. An analysis of the mortality within the relict population of P. nobilis in the Mar Menor lagoon after the last population survey in 2019 has been carried out, together with a characterisation of some microscale factors that describe its current habitat in the lagoon. For this purpose, three sampling localities were selected along the east coast of the lagoon, where a study of both live and dead individuals was conducted. Additionally, a characterisation of the macrophyte beds and the sediment conditions surrounding these individuals was carried out, comparing the sediment near the recently dead and live individuals. All studied localities exhibit similar mixed macrophyte beds of Cymodocea nodosa (Ucria) Asch., 1870 and Caulerpa prolifera (Forsskål) J.V. Lamouroux, 1809. At the location where significantly less C. nodosa cover was observed, the mortality of P. nobilis individuals was higher, and the sediment near the dead individuals was also more disturbed (with a more negative Eh and higher percentage of organic matter). These results contribute to a better understanding of the dynamics of microscale factors following P. nobilis mortality events, facilitating the identification of potential survival areas.