The introduction of non-indigenous fish species (NIFS) to freshwater ecosystems is considered as one of the leading factors associated with freshwater biodiversity loss. Unravelling the spatial overlap between NIFS and critically endangered (CR) fish species can contribute to targeted conservation planning and actions to minimize the potential negative effects. In this study, we applied a geostatistical analysis of species distribution data to investigate the potential overlapping areas of NIFS against fish species that are designated under a CR status according to the International Union for the Conservation of Nature (IUCN) and the Hellenic Zoological Society (HZS) Red Lists. Distributional (presence–absence) data of all NIFS were compiled for both lentic and lotic ecosystems of Greece. In total, 800 sites were utilized from 169 lakes and 631 river sites from 51 river basins. Our results indicate that freshwater ecosystems under high NIFS richness are located mainly in lowland areas of western, central and northern Greece usually near large cities and ecosystems with high commercial and recreational fisheries. On the contrary, low NIFS richness was observed in mountainous regions and small river basins. Overlapping areas of CR species with moderate to high NIFS richness (1.5-4.3 NIFS per 1 km²) were relatively high (~50%). Many of the overlapping areas fall well within NATURA 2000 network, where legal management bodies can implement management programs to minimize the negative impacts. However, some areas of conflict are in unprotected zones and may be likely to experience significant negative biodiversity impacts. The use of the CR status is useful as a proxy indicator for some of Greece's most important inland water ecosystems in order to avoid new invasions and to manage established alien and translocated species. Our findings demonstrate that many freshwater ecosystems in Greece are under significant invasion pressure and also exhibit high biodiversity conservation value.