Compared to traditional hard engineering, nature-based flood protection can be more cost effective, use up less raw materials, increase system adaptability and present opportunities to improve ecosystem functioning. However, high flood safety standards cause the need to combine nature-based structures with traditional civil engineered structures. This increases complexity assessing when and how ecological and engineering objectives of such flood protection systems are achieved. This study classifies the degree to which coastal designs are nature based using criteria for ecosystem-based management (EBM). For the engineering criterion the distinction between main and supporting structures is introduced. To evaluate the ecological criterion five design concepts have been introduced, ranging from completely engineered to completely nature-based. The method results in an EBM-ranking of the coast, showing where a particular flood protection design stands on the range between completely engineered (low EBM-rank) and nature-based (high EBM-rank). It thus facilitates comparison of different flood protection systems. The method was the applied on the North-Sea coast of Belgium, the Netherlands, and Germany. The results show that combinations of civil-engineered and nature-based structures are widely applied. However, due to the overall low contribution to flood protection by the nature-based structures, about 85% of the coast is dominated by engineered structures. The majority of these stretches is located in relatively sheltered areas. Improving the flood protection capacity of the nature-based structures in these areas is hard to achieve. Therefore, application of more nature-based design concepts on the main structures is the most promising way to improve the EBM-rank of many flood protection systems.