Watercourses are often impacted by hydraulic infrastructures and water withdrawals. It has been demonstrated that these alterations affect the availability of habitats for aquatic species. Consequently, it is necessary to define a method to quantify the effects on the species and to define the proper e-flow level required to ensure the conservation of the biodiversity and the ecological services provided by the rivers. Therefore, for the e-flow definition, the Meso-HABSIM methodology (Mesohabitat SImulation Model) [1, Parasiewicz, 2001] is adopted in Italy. It is a well-established method for the river habitat modelling, designed to assess the spatial and temporal habitat availability for fish fauna.