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A new approach, the ‘Naturalness Status' (NS), is suggested to classify the hydrologic alteration of temporary rivers from natural conditions based on the Hydrological Status Tool (HS-Tool). The HS-Tool considers two metrics: the degree and the predictability of dry flow conditions for both natural flow and its alterations, at each water body in actual and natural conditions. The Soil and Water Assessment Tool (SWAT) model is simulating the river flow of Evrotas water bodies, Greece, under natural, actual and climate-impacted conditions. The majority of Evrotas water bodies (72%) experience good (low-impacted) NS for the examined period (1990–2010), despite their intermittent flow regime. Severe flow alteration is predicted for 57% of Evrotas water bodies (high-impacted NS), while selecting the KNMI-RACMO2 future climate projections scenario (2020–2060) as input into the SWAT model. Hydrologic extreme drought phenomena or anthropogenic pressures in water regime can be quantified by the NS. The method is intended to be used in basin decision-making analysis at fulfilling the Water Framework Directive goals. [ABSTRACT FROM PUBLISHER]