Freshwater biodiversity has shown to be highly vulnerable to climate warming. Boreo-alpine species are especially at risk in the Alps because they have to migrate to higher elevations to avoid local extinction. Effects of climate warming could be partly counteracted by creating new freshwater habitats: this would boost the population sizes of the endangered species and would increase the connectivity between Alpine waterbodies to facilitate the species’ upward dispersal and colonization of new habitats. Nevertheless, the localization of new habitats has to be carefully chosen, as successful restoration (or habitat creation) depends on many abiotic and ecological variables (e.g. habitats density and quality, connection between bodies of water, presence of targeted species, resistance of landscape to species movements). Furthermore, various socioeconomic drivers and actors determine the land and water uses in the Alps. Therefore we developed an innovative method for prioritization of areas for creation (or restoration) of small bodies of water, taking into account both ecological parameters (from species to landscape) and social ones. The method was developed in a test area (130 km2, in Canton Valais, Switzerland) representative of the Swiss Alpine landscapes and their associated socioeconomic activities. The proposed methodological framework consists of four steps which allow refining the geographical area to propose two or three small areas (some hectares) suitable for the creation of small water bodies. The first step investigates the regional scale, often several thousand km2, with a focus on environmental considerations: presence of historical or contemporary wetlands and waterbodies, presence of cold stenotherm species, and favourable landscape (in terms of land use) and socioeconomic context. The second step identifies areas of biological connectivity between source ponds and future host ponds for cold stenotherm species, taking into account the distance between source and host ponds and landscape resistance to the movements of propagules, finally highlighting the migration corridors. The third step checks the preselected areas with the aim of discarding catchments impaired by selective or diffuse pollutions. The fourth and final step is intended to enhance the probability of the project’s social acceptance: qualitative interviews and field observations are conducted on a local scale (often one km2) and options are evaluated with local stakeholders. Conducting the four successive and complementary steps ensures that the selected areas have a high potential for hosting the alpine biodiversity, and furthermore provide a favourable social framework for success in the short as well as the long term. Such a tool should promote and facilitate actions for conserving freshwater biodiversity in the Alps.