For the first time a palaeobiogeographic framework is proposed for European Neogene freshwater systems. The distribution of 2,226 species-group taxa of freshwater gastropods from over 2,700 Miocene and Pliocene localities was evaluated. The localities were grouped into palaeo-freshwater systems based on latest palaeogeographic reconstructions. Cluster analyses were computed for four time slices, i.e., Early Miocene, Middle Miocene, Late Miocene, and Pliocene. The analyses demonstrate a generally high degree of provincialism for the Neogene freshwater systems and allow the definition of biogeographic units. The delimitations are based on the cluster analyses, the degree of endemicity, and geographical coherence. The Early Miocene is characterised by a relatively low degree of provincialism suggesting the distinction of three regions. Coinciding with the development of many endemic systems on the Dinarian-Anatolian Island and in central Europe, the Middle Miocene demonstrates a higher degree of provincialism, allowing the definition of six biogeographic regions. With the onset of the Late Miocene the retreat of the Central Paratethys and development of the huge Lake Pannon massively shaped faunal evolution and palaeobiogeography in general. The formation of the 'Lago-mare' environment fringing the Mediterranean Basin as well as the development of several restricted freshwater systems in Western Europe additionally promoted biogeographic division. The increasing provincialism allowed the delimitation of six biogeographic regions, three of which could be subdivided into seven dominions. With the disappearance of Lake Pannon and the decline of western European and Mediterranean faunas at the Miocene-Pliocene boundary, biodiversity hotspots shifted toward eastern and southeastern Europe. For the Pliocene, four biogeographic regions, five dominions, and four provinces were defined.