As many large rivers in Europe, the Rhône river in France has been heavily regulated during the last two centuries. Following a number of initiatives, a 10 year restoration program of the river started in 1998. It involved increased minimum flows below eight dams along the river. A strong collaboration between scientists, managers and decision makers made it possible to define a consistent monitoring of the different restoration operations, and to develop shared tools for assessing their ecological effects. Focusing on fish communities in the main channel of the river, the scientific knowledge of their dynamics is variable across sites. Where fish have been surveyed during more than 20 years, as in the Upper Rhône region upstream from the city of Lyon, trends in community structure can be observed, showing that the effects of the restoration have to be interpreted in a larger spatial and temporal context. The Rhône river restoration program is a unique occasion for testing the predictability of the impact of hydraulic changes on fish community, because instream habitat models where run in all sites before restoration. The minimum flow has been already modified below three dams in the river, starting with the dam of Pierre-Bénite just below the city of Lyon (minimum discharge was increased from 10 m3/s to 100 m3/s in 2000). We observed a shift in fish community structure at Pierre-Bénite, with a proportion of fluvial specialists (barbel, nase, spirlin, stream bleak, dace) changing from 17% before restoration to 36% after. This change was dynamic and was largely due to young individuals, suggesting modified conditions for the reproduction. It confirmed the blind quantitative predictions of the instream habitat models.