There is extensive experience in adaptive management of exposed sandy coastlines through sand nourishment for coastal protection. However, in complex estuarine systems, coastlines are often shortened through damming estuaries to achieve desired safety levels. The Dutch Deltaworks illustrate that this approach disrupts natural sediment fluxes and harms ecosystem health, which negatively affects derived ecosystem services, such as freshwater availability and mussel and oyster farming. This heavily impacts local communities and thus requires additional maintenance and management efforts. Nevertheless, the discussion on coastline shortening keeps surfacing when dealing with complex coastal management issues throughout the world. Although adaptive delta management accompanied by innovative approaches that integrate coastal safety with ecosystem services is gaining popularity, it is not yet common practice to include adaptive pathways, a system-based view and ecosystem knowledge into coastal management projects. Here, we provide a first attempt to integrate ecosystem-based flood risk reduction measures in the standard suite of flood risk management solutions, ranging from structural to non-structural. Additionally, for dealing with the dynamic and more unpredictable nature of ecosystems, we suggest the adaptive delta management approach that consists of flexible measures, measurable targets, monitoring and intervention, as a framework for embedding ecosystem-based alternatives for flood risk mitigation in the daily practice of engineers and coastal planners.