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A geographical information system (GIS) for freshwater crabs and fishes in Greece was created in response to the European Environmental Agency's (EEA) biodiversity initiative for European Union countries. A total of 1931 collections, made with seines, dipnets, and backpack electroshockers in 32 drainages of Greece, yielded 126 species of fishes and crabs in 2,359 data records including species, latitude, longitude, drainage, prefecture, and locality, 731 also include stream order, elevation, gradient, stream width and depth, pH, temperature, and distance to river mouth. Our GIS indicates current distributions of species, species rich and poor areas, anomalous species distributions, areas warranting further sampling, and cogeneric species whose overlapping ecological distributions call for taxonomic and phylogenetic investigation. In applied studies, the freshwater GIS can be an integral tool for EEA's biodiversity inventory of the southern Balkan peninsula, an inland fisheries management plan, designs for environmental impact studies, and conducting gap analyses for the region.