AbstractFreshwater mussels, historically a component of freshwater benthic invertebrate biomass, are one of the most imperilled animal groups on the planet.Margaritifera auriculariawas once a common freshwater mussel inhabiting large rivers throughout Western Europe. It was believed to be extinct until 1996 when a few small populations were found in Spain and France.CurrentlyM. auriculariais one of the most endangered species in the world. The current status of this mollusc in the Ebro River was surveyed, finding a few adult specimens at only two localities, and many old, empty shells throughout the river.Using a simple analysis of historical hydrological data, dramatic changes in water flow might have led to localized extirpation of this freshwater mussel.Other factors contributing to the slow extirpation of this long‐lived invertebrate from other areas of the Ebro Basin include the continuous reduction of water levels during the reproductive season, overharvesting for nacre, construction of impoundments, extinction of fish hosts, and impaired water quality.Copyright © 2016 John Wiley & Sons, Ltd.