This paper aims to frame the multi-layered water safety concept in the context of a systematic, thorough, multidisciplinary and collaborative methodology for complex problems solving, i.e. geodesign. Multi-layered safety is an integrated flood risk management (FRM) concept based not only on flood probability reduction through prevention (layer 1), but also on consequences’ minimization in the case of a flood through spatial solutions (layer 2) and crisis management (layer 3). It has been introduced in the Netherlands in 2009 following the European Flood Risk Directive adopted in 2007. In this study, the multi-layered safety is qualitatively assessed, demonstrating that it rather resembles a parallel system, and that collaboration is required to decide about the most desirable safety measures, which should not only be based on their economic efficiency but also on their social acceptability. In the light of these factors, we attempt to methodologically systematize the multi-layered safety concept by following the geodesign framework. The latter means that, through its implementation, understanding of the current situation of a particular area of interest, which in turn it may support, the allocation of weights regarding the three layers of the multi-tier safety concept is facilitated. Furthermore, the geodesign of the multi-layered safety shows that participation and interaction of the safety policy makers, as well as iterations for achieving maximum consensus between them concerning the more balanced safety measures, taking into account their economic efficiency, their impact on the environment, the local circumstances and the values of the people at place, are methodologically enabled.