Riparian zones are some of the most valuable and at the same time endangered ecosystems in the world. Their progressive degradation caused by anthropogenic pressure calls for the adoption of effective, resilient restoration strategies. However, a full understanding of the complex mechanisms governing riparian ecosystems has not yet been achieved, and many assumptions are based on qualitative findings. We quantitatively investigated the habitat conditions of a key riparian plant, the German tamarisk (Myricaria germanica), using a two-dimensional hydrodynamic model that was created for a braided reach of the river Sense (Switzerland). The results demonstrate that the presence of this species in gravel bar habitats is strongly correlated with inundation frequency. The species was present on gravel bars near the main river channels, which are inundated every 4–5 years. Where the gravel bars are frequently flooded, seedlings do not survive the hydrodynamic perturbations, whereas elsewhere, where periodic flooding does not reach, M. germanica is replaced by stronger competitors. Our study contributes to an understanding of the dynamics of riparian corridors and provides a quantitative basis for developing effective restoration plans, which may involve the optimisation of hydropower regulation programmes.