Integrated ecosystem management is challenging due to many, often conflicting, targets and limited resources to allocate. A valuable and straightforward approach is to integrate an ecosystem services assessment in a cost-effectiveness analysis as method to evaluate and compare the cost-effectiveness of several management scenarios to reach one or more objectives and take into account the potential effects on other ecosystem functions and services. Nevertheless, this method is not commonly used in ecosystem management evaluation but can provide an alternative for the frequently used but often contested cost-benefit analysis (which requires the step of assigning a monetary value to each benefit). The aim of this study is to apply the cost-effectiveness analysis in combination with an ecosystem services assessment on a real case-study (comparing alternative management strategies for estuaries) to derive lessons learned to go from theory to practice. The application of this method for the case-study reveals many remaining challenges such as data availability and knowledge to assess ecosystem effects of management measures. Nevertheless, the analysis demonstrates that this method can be used for making a more integrated evaluation and supporting better-informed management decisions. Display omitted •An ecosystem services assessment is integrated in a cost-effectiveness analysis.•The method is applied on 4 management alternatives in estuaries.•Despite data limitations, the cost-effectiveness is calculated for four ecosystem services.•The main challenge of assessing management effects is finding a common indicator.•Flood control areas are more cost-effective than traditional dikes.