To address the global loss of biodiversity in freshwater environments, understanding river habitat requirements for key species, such as brown trout (Salmo trutta L.), is crucial. The Habitat Suitability Index (HSI) aids ecologists in identifying preferred habitats, considering parameters like flow velocity, water depth, and substrate type. Monitoring river reaches for suitable conditions is time-consuming, prompting the need for efficient alternatives. This work proposes an enhanced HSI incorporating macroroughness (e.g., boulders) during low-flow conditions, which are crucial in alpine rivers. Building upon a recent model from the literature, it integrates the distribution of wakes from obstacles, creating a comprehensive HSI. This correction reveals additional peaks in HSI curves during low flows, emphasising the spatial importance of large stones. Importantly, the proposed approach easily converts HSI to Weighted Usable Area (WUA), determining the actual suitable area for brown trout to live.