The European Floods Directive requires member states to prepare flood risk management plans for their river catchments. The first generation of those plans was just developed at the end of 2015; the next revision is due in 2021. The new instrument institutionalizes an ongoing paradigm shift from flood protection to flood risk management in Europe. It implies two major governance challenges: the spatial turn and the scenario approach. This contribution studies the implementation of these two governance challenges in the Netherlands, where the paradigm shift is considered to be advanced. Therefore, the spatial turn and the scenario approach are operationalized. The spatial turn consists of three aspects: space for the river, an integrated approach, and beyond structural measures. The scenario approach introduces the vulnerability of society in flood risk management. It is discussed how the challenges of spatial turn and the scenario approach—and thus the shift towards flood risk management—have an effect on the prevailing modes of governance in water management in the Netherlands. This helps understand the tensions and frictions with implementing the plans, but also illustrates how the European Floods Directive institutionalizes the shift towards flood risk management. The analytical scheme, consists mainly of operationalization, can foster future comparative studies with other countries and over time, to trace the changes in approaches to flood risks in Europe.