1. Instream habitat models are attractive tools for assessing the impacts of flow restoration on aquatic organisms, but have been rarely used for invertebrates due to the lack of knowledge of their hydraulic preferences. 2. In this study, we provide quantitative models of the hydraulic preferences for 66 invertebrate taxa found in the Upper Rhône River (France), and combine these preferences with a statistical habitat model (FSTress) to predict the effects of minimum flow restoration on invertebrate abundances in two bypassed sections of the river. 3. Many taxa show marked preferences for particular hydraulic conditions. Average preferred hydraulic conditions were significantly related to those observed in smaller streams (R2 = 0.37). 4. Our model predicted that habitat values of 27 taxa should be enhanced by restoration operations, but also predicted a decrease of habitat values in the main channel for 12 limnophilic taxa. However, these taxa are expected to maintain populations by finding refuges in restored cut-off channels and overall invertebrate diversity is predicted to increase in the two bypassed sections studied here