This study aimed to set out a new methodology for habitat modeling in high-gradient streams. The methodology is based on the mesoscale approach of the MesoHABSIM simulation system and can support the definition and assessment of environmental flow and habitat restoration measures. Data from 40 study sites located within the mountainous areas of the Valle d'Aosta, Piemonte and Liguria regions (Northwest Italy) were used in the analysis. To adapt MesoHABSIM to high-gradient streams, we first modified the data collection strategy to address the challenging conditions of surveys by using GIS and mobile mapping techniques. Secondly, we built habitat suitability models at a regional scale to enable their transferability among different streams with different morphologies. Thirdly, due to the absence of stream gauges in headwaters, we proposed a possible way to simulate flow time series and, therefore, generate habitat time series. The resulting method was evaluated in terms of time expenditure for field data collection and habitat-modeling potentials, and it represents a specific improvement of the MesoHABSIM system for habitat modeling in high-gradient streams, where other commonly used methodologies can be unsuitable. Through its application at several study sites, the proposed methodology adapted well to high-gradient streams and allowed the: (1) definition of fish habitat requirements for many streams simultaneously, (2) modeling of habitat variation over a range of discharges, and (3) determination of environmental standards for mountainous watercourses.