Altered river reaches are causing important loss in freshwater biodiversity and habitat availability. To face this problem, river restorations are gaining increasing importance in the scientific community, leading to the need for better and more precise tools able to predict and evaluate the outcomes of these measures in terms of both habitat quality and fish population responses. This study presents a method to determine the improvement in habitat quality for different brown trout (Salmo trutta L.) life stages in a river network. By coupling Habitat Suitability Curves with Manning’s equation to estimate water depth and flow velocity from data on flow discharge, it is possible to compute the compound Habitat Suitability Index for both pre-and post-restoration conditions. Following a novel approach present in the literature, a further step is taken by incorporating the contribution of macro-roughness elements (e.g., boulders) in the habitat model. Results indicate that integrating macro-roughness features significantly enhances habitat availability and quality, making their contribution pivotal in the evaluation of restoration outcomes. This method can be then incorporated with metapopulation models, offering a practical and efficient tool for scientists and experts to plan and evaluate restoration projects.