Habitat simulation models are effective tools which can be used to estimate spatial and temporal habitat availability for aquatic organisms, and to design and evaluate habitat restoration actions. Based on the meso-scale resolution, the present work proposes two indices to evaluate the spatial and temporal alteration of instream habitats. Firstly, the Index of Habitat Quantity (IHQ) describes the relative amount of habitat loss due to flow diversion, and, secondly, the Index of Habitat Stress Days (IHSD) measures the increase of continuous duration of events when habitat bottlenecks create stress to the fauna. Two case studies from the mountainous areas of Northern Italy are presented as applicatory examples. The achieved results indicate that (i) the meso-scale can be considered an appropriate scale resolution to link fish habitat requirements to fluvial morphological characteristics, and (ii) the proposed indices are flexible tools since they can capture both spatial and temporal alterations of habitat structure and can be applied to different kind of pressures (e.g., hydropower generation, hydropeaking).