Human induced-physical habitat alterations are the main threat to aquatic ecosystems. In a context of climate change, these alterations could be exacerbated by changes in low flow regimes, inducing modifications of aquatic communities. Understanding the links between aquatic communities, their physical habitat and climate change is therefore a major but difficult challenge because climate change can interact with other anthropogenic pressures, thus confounding their effects. In this study, we simulate potential macroinvertebrate hydraulic habitat alterations due to predicted more extreme low flows on the Loire River watershed, regardless of other anthropogenic pressures. By coupling a species distribution model and a habitat model that combines a model of shear stress distribution with a macroinvertebrate preference model, we are able to point out changes in community structure in response to shifts in habitat availability. By isolating more extreme low flows effects on macroinvertebrate communities, we emphasize natural sensitivities to climate change and provide a frame to better understand how anthropogenic pressures could exacerbate them.