Major flooding events frequently affect multiple countries located in the same river basin, making flood mitigation a crucial concern in these areas, particularly in transboundary regions. France and Germany have historically shared experiences regarding flood risk management, drawing on both their differences and commonalities. However, there is a lack of research concerning the challenges and perspectives related to the implementation of flood risk management strategies in these countries. This study determines the integration of flood-related concerns into spatial planning in the European context through a comparative case study. The research was conducted by collecting secondary data from various sources to examine a comparative analysis of the effectiveness of the existing legal and institutional frameworks for flood management in these two countries. The analysis evaluated three criteria: 1) the legal and institutional framework for managing flood and flood-related issues, 2) progress in implementing national flood mitigation strategies, and 3) international cooperation in transboundary regions within the context of the European framework for flood risk management. The study’s findings reveal several key factors that contribute to effective flood mitigation strategies. Firstly, the spatial planning system plays a crucial role in achieving the fundamental goals of national flood mitigation strategies, with decentralized power and autonomous planning at the local level being essential drivers. Secondly, coordination is identified as a critical factor. Both systems employ comprehensive approaches that integrate non-structural measures with existing structural measures. Finally, international cooperation is shown to evolve from voluntary to mandatory (via binding agreements) due to the need to address multilateral issues through institutional change.