1. The critically endangered fan mussel Pinna nobilis, endemic to the Mediterranean Sea, faces a drastic population decline all over the Mediterranean Sea owing to an infectious disease.2. Coastal lagoons represent one of this species' last reservoirs; thus, knowledge of the population conservation status in these ecosystems is essential.3. An extensive monitoring programme was conducted during 2014, 2017 and 2019 in the Mar Menor lagoon, a highly eutrophicated lagoon from Spain. On average, 32,535 m 2 have been surveyed each year to determine population densities, distributions and size structures.4. The cumulative impacts produced by intensive agriculture activity around the lagoon, together with a catastrophic meteorological phenomenon that occurred in 2019, have triggered a significant decline in fan mussel population densities and in population mean shell sizes over the years. Additionally, some fan mussels were infected by the protozoan Haplosporidium pinnae.5. Therefore, the current P. nobilis population from the Mar Menor is mainly composed of young individuals in specific areas that are facing an extreme situation. Urgent management and conservation actions focused on restoring the ecosystem and protecting P. nobilis individuals are urgently needed, together with reinforcement projects to increase the species' stock in one of its last reservoirs.