The navigation waterways to the harbors of Rostock (Warnow Estuary), Germany, and Szczecin (Oder/Szczecin Lagoon), Poland, were recently deepened. Both activities required Environmental Impact Assessments. We conducted expert- and data-based ecosystem service assessments for both case studies. Additionally, we performed 3D-ecosystem model simulations. For the Oder Lagoon, the model results show that the waterway deepening increased the burial in sediments by 807 t N/a, 112 t P/a and 4661 T C/a. However, altogether, the impacts of the deepening to 12.5 m draught on the lagoon ecosystem are minor and a model application is not necessary, but the results improve the data basis for ecosystem service assessments. Our expert-based ecosystem service approach is adaptable to the needs of coastal engineering and hydraulic projects and is both easy and quick to apply and transferable. The assessment results highlight the relevance of cultural services and can complement EIAs. Our approach can especially support the early scoping stage of an EIA. It has the potential to enhance cooperation and communication with and between stakeholders, reduce conflicts, and save time. Additionally, it could improve the compilation and addressing of stakeholder concerns, potentially reducing costs associated with unnecessary studies.