Aim: The maintenance of broad-scale connectivity patterns is suggested as a sustainable strategy for biodiversity preservation. However, explicit approaches for quantifying the functional role of different areas in biogeographic connectivity have been elusive. Freshwaters are spatially structured ecosystems critically endangered because of human activities and global change, demanding connectivity-based approaches for their conservation. Mass effects—the increase in local diversity by immigration—and corridor effects—the connections with distant communities—are basic and relevant mechanisms connecting diversity with landscape configuration. Here, we identified freshwater hotspots areas for mass and corridor effects across Europe. Location: Europe. Methods: Using satellite images, we quantified the areas of ephemeral, temporal and permanent freshwaters. The landscape structure of the freshwater ecoregions was represented as a directed-graph, and the link weights were determined by the distance between cells and the water cover. Three centrality metrics were used to rank freshwater areas with respect to their potential role in dispersal-mediated mechanisms. Out-degree represents the potential of an area to operate as a diversity source to other regions. In-degree reflects the importance that incoming dispersal may have in local diversity. Betweenness refers to the importance of local areas for connecting other distant areas. Results: We detected great concentrations of source hotspots on the northern re- gions associated to lentic ecosystems, main European rivers acting as ecological corridors for all freshwaters, and a mixed distribution of connectivity hotspots in southern and Mediterranean ecoregions, associated with lentic and/or lotic systems. Main Conclusions: We showed an explicit connection between landscape structure and dispersal process at large geographic scales, highlighting hotspots of connectivity for the European waterscape. The spatial distribution of hotspots points to differences in landscape configurations potentially accounting for biogeographic diversity patterns and for mechanisms that have to be considered in conservation planning.