Although freshwater molluscs in the order Unionoida are considered one of the most endangered groups of animals in the world, sufficient data on their status are lacking for most species. As a result, a species may become rare, endangered, and even extinct before the first population assessment is conducted. This is especially true for endemic species, particularly those limited to remote regions with difficult access. We studied the current distribution and population densities of Popenaias popeii endemic to the Rio Grande drainage in Texas, and developed a method to evaluate changes in the population’s size and distributional range over the last 100 years. Sampling over 250 sites in four rivers that constitute the entire historical range of P. popeii in Texas, we found that this species has likely been extirpated from two rivers. The total length of the rivers populated by this mussel has declined by 75%, and the total P. popeii population size has declined by 72%. The remaining population of this species in the Rio Grande is fragmented, with only one 190-km stretch still supporting high densities. The developed approach could be used for other rare freshwater molluscs to reconstruct their historical range and population size.