Policy makers are confronted with the question how to combine sustainable flood protection and floodplain rehabilitation in the best possible way. Both topics deal with spatial planning aspects in a range of scales. This question was the starting point for the development of an evaluation method within the IRMA/SPONGE project INTERMEUSE, illustrated on the basis of assumed flood protection strategies in the Meuse river basin (the “sponge” strategy, the “retention” strategy, and the “floodplain lowering” strategy). The integration of flood protection and floodplain rehabilitation can be performed on two scale levels that are interrelated: on the regional level the focus is on (large parts of) an entire stream basin, on the local level specific site conditions are taken as starting point. Ecological aspects under study are spatial cohesion of habitats as identified by species population persistence modelling (regional, longitudinal level) and required habitat quality for carabid beetles and for meadow vegetation gradients as assessed by correspondence analysis (local, transversal level). The carabid beetles are taken as indicative for the ecological integrity of the river bed, the meadow vegetation for that of the floodplain. Unifying concept in the evaluation of ecological integrity is the ecological minimum: the critical boundary or minimum level of habitat conditions for a potentially good ecological functioning. It is the least acceptable state for a river ecosystem that is still functional to some extent, compared to a natural river ecosystem. The results of this study show clearly that there is a good chance to combine floodplain rehabilitation aims with flood protection activities, both on a local and on an international scale. Although ecological effect assessment and ecological optimising (referring to a natural reference state) remain basic, additionally the assessment of the ecological minimum helps defining design strategies for integrated flood protection, especially in situations where river rehabilitation is an opportunity.