Here, we show for one of the Dutch Rhine River branches that large-scale riverine ecosystem rehabilitation and related vegetation succession may lead to up to 0.6 m higher river flood levels, because of increased hydraulic roughness. We hydraulically modeled future succession stages of embanked floodplain vegetation, following from present ecosystem rehabilitation plans for the 124-km-long river IJssel, and found flood levels exceeding the safety levels (related to dike heights). Our models take into account river engineering measures that are presently carried out, aimed at enhancing the river discharge capacity in order to meet required safety standards. Our study shows that there is a pressing need for integrated hydraulic-ecological evaluation of river engineering measures and ecosystem rehabilitation plans in the Rhine embanked floodplains. An important conclusion also is that hydraulic evaluation of planned vegetation goals only is inadequate, because flow resistance of preceding succession stages may be higher.