The species of the Ponto-Caspian gastropod genus Clathrocaspia Lindholm, 1930 have been recorded so far from the Caspian Sea Basin only from marine waters, whereas they inhabit the estuarine areas as well as the purely freshwater environments in the Azov–Black Sea Basin. This genus has recently been assessed as putatively extinct in the Caspian Sea. A new purely freshwater species Clathrocaspia laevigata sp. n. from the water-flows of the Samur River delta in Dagestan, Russia, is described. A morphological comparison of the new species with C. brotzkajae (Starobogatov in Anistratenko & Prisjazhnjuk, 1992) from the Caspian Sea and C. knipowitschii (Makarov, 1938) inhabiting the Azov–Black Sea Basin shows their overall similarity. The major difference is that C. laevigata sp. n. almost completely lacks the reticulate teleoconch sculpture, whereas it is well-developed in all known Clathrocaspia species. The molecular data revealed probable sister relationships between the new species and C. knipowitschii. All Dagestan populations are ecologically and spatially isolated from the open sea and and are very locally restricted. We suggest to consider newly described snail species as retained in a pure freshwater refuge located in the coastal area of the Caspian Sea. The discovery of such a refuge sheds more light on the origin, current state and the future of the unique Ponto-Caspian aquatic biota under global change and increasing anthropogenic impact.