In the current context of climate change, water is becoming an increasingly contested resource, requiring tools that can balance human uses—domestic, agricultural, and hydroelectric—with the maintenance of good ecological status, as required by the European Water Framework Directive 2000/60/EC. One such tool is the MesoHABSIM methodology, which can help determine Environmental Flow conditions for river reaches based on habitat availability for aquatic species. In Italy, the methodology has been officially adopted since 2017, and published in the ISPRA Technical-Operational Manual 154/2017. Furthermore, in the Aosta Valley region, it has been incorporated into the strategic water protection plan and is employed within a multicriteria analysis framework to support decision-making processes concerning riverine habitat management and ecological flow assessment.