1. Freshwater ecosystems in Europe are increasingly under threat due to climate change, land-use intensification, and biodiversity loss – posing serious risks to critical ecosystem services.2. Restoration of freshwater ecosystems is essential for achieving EU policy goals, including the European Green Deal and the Biodiversity Strategy, while enhancing ecological resilience and sustainability.3. The MERLIN modelling workflow, developed under Work Package 3, provides a structured, scalable approach to assess both biophysical and economic impacts of restoration across Europe.4. Based on the open-source SWAT+ tool, the workflow integrates ecohydrological modelling with ecosystem service analysis and socio-economic valuation to support evidence-based decisionmaking.5. It uses harmonised, EU-wide publicly available datasets, making it applicable even in data-scarce regions and adaptable to both local and continental scales.6. The tool simulates a wide array of restoration measures –including wetland rewetting, riparian buffers and floodplain reconnection –offering insights into ecosystem service trade-offs and synergies.7. A distinguishing feature of the MERLIN workflow is its capacity to conduct a monetary valuation of restoration benefits and improved policy alignment.8. This user-friendly, step-by-step guidance is designed for a wide audience – from field practitioners to policymakers – and supports various technical skill levels.9. Early implementation shows the workflow’s flexibility and potential to improve restoration planning, with opportunities for enhanced accuracy through integration of local, high-resolution data.