This paper presents the results of a study which characterizes the hydrological regime of a temporary river at reach scale and analyzes the hydrological alterations due to anthropogenic pressures using the SWAT model to estimate the daily streamflows and the periods without flow which would occur in natural conditions. The study area is the Salsola and Celone river basins, located in SE Italy. In a first part, we identified six classes of flow, the so-called Aquatic States (ASs), which play a major role in determining the available mesohabitats and subsequently the characteristics of the aquatic life. The monthly occurrence of the different ASs over a long period has been evaluated in order to provide useful information to design biological samplings. The results show that dry bed conditions can occur from May to January and arheic state from April to January in the reaches located in the upper part of the basin. The impacted river reaches showed a different behavior depending on the anthropogenic impacts. In a second part, two indicators based on the statistics of the periods without flows were used, monthly flow permanence and dry season predictability, for describing the flow regime components which may have been altered by anthropogenic pressures. The indexes, which were computed in impacted and natural conditions, were used as coordinates in a plot to obtain a graphical vision of the regimes. The distance between the points representing the actual (impacted) and natural states in the plot were used to classify the hydrological alterations.