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Objectives were to test the hypothesis that stream order and stream width alone account for species diversity in drainages of Greece, and to create a mathematical model that predicts fish diversity in small and medium sized freshwater streams in the southern Balkan Peninsula in accord with the stream classification system proposed by the European Environmental Agency (EEA). Thirty-seven species of fishes in 12 families (Petromyzontidae, Anguillidae, Cyprinidae, Moronidae, Centrarchidae, and Blenniidae) were collected in five stream orders (1-5) from 19 river drainages in Greece in 1993 and from 2000-2002. Numbers of species were significantly correlated with stream order (+), width (+), and depth (+), and elevation (-). Results of stepwise regression indicated that stream order, elevation, stream depth, and river km were significant factors associated with ichthyofaunal diversity, and were used to create a regression model to predict species diversity (up to 5th order streams). We conclude that geo-specific factors (i.e., small, isolated drainages with limited water budgets, geological history, dry climate, and low annual rainfall) should be included in the EEA monitoring design for lotic waters in harsh environments of southern Mediterranean countries as these features differ from those of central, eastern, and northern European countries with larger watersheds.