Multifunctional use of flood defences is seen as a promising solution for improving the synergy between flood protection and urban development. Combining the functions can, however, create unintended dependencies, which can influence the desired performance of the system in unexpected ways. Recognising the risks associated with these dependencies early during the conceptual design phase can help to improve the system capability to mitigate the resulting threats and to take advantage of the opportunities created. This paper examines the use of the ‘Functional Resonance Analysis Method’ (FRAM) for qualitative risk analysis of multifunctional flood defences. The method is customised and applied to a case study of a multifunctional flood defence in the Netherlands. The analysis results are used to identify the threats and opportunities that need attention during the design of a multifunctional flood defence and to propose recommendations for how to address them. It is concluded that FRAM can serve as a useful complement to the reliability analysis methods for enriching the risk analysis of multifunctional flood defences.