Over the last centuries, the Rhône River has been deeply modified by numerous uses and activities like navigation, irrigation, fight flooding, hydroelectricity production... Embankment, dams and groyns constructions, water diversion, and secondary channel artificial cut-off generated morphological changes such as channel degradation and narrowing, bank stabilization, and former channel terrestrialisation. These changes result in a fundamental modification of flowing conditions during floods and connections between channel and floodplain ecosystems. Within the framework of compensatory measures, the CNR (Compagnie Nationale du Rhône, i.e. the Rhône River manager) wants to carry out a restoration project along the downstream reach of the Rhône River (southern France, 100 km length upstream from the mouth). The ambition is to combine both a decrease in local flood risk (by enlarging flood-carrying capacity) and an enhancement of geomorphological and ecological properties of the margins into the reach (sediment reworking, pioneer species regeneration...). The Rhône River is a good case study for complex and deeply altered systems. Indeed, important issues have to be integrated: (i) flood risk for the major city along the reach (Arles), (ii) bank erosion control near cultivated areas, (iii) former channels loss of diversity due to terrestrialisation processes and floodplain forest deconnection because of the channel degradation, (iv) pollution risk if polluted sediments are reworked (contamination by metals, PCB and radionuclides), (v) navigation, and (vi) sediment deficit that impacts coastal evolution downstream the reach (Camargues delta). We present a step-by-step strategy to reach an equilibrium between human activities and ecological purposes. All aspects are discussed: can historical state be considered as a reference-state? How can we choose sites to test the actions? How to design these actions? Which monitoring strategy has to be developed? Which kind of ecosystems can be expected under Mediterranean climate (composition, recovery rate, presence of exotic species...)?