The study explores the application of a Theory of Change (ToC) framework in 18 large-scale freshwater restoration projects within the context of the European Green Deal and the recently adopted Nature Restoration Regulation. By leveraging a participatory approach, the research examines the effects of freshwater restoration measures across three ecosystem clusters: peatlands and wetlands, small streams, and large rivers. In a conceptual model, restoration measures were connected with transdisciplinary goals, assessing biophysical, social and economic outcomes. The findings highlight the effectiveness of Nature-based Solutions in advancing climate resilience, biodiversity gains, and social equity while identifying potential trade-offs and negative effects. The ToC framework proved valuable in guiding restoration planning, facilitating stakeholder engagement, and enabling adaptive management in accordance with the Nature Restoration Regulation’s requirements. However, the study underscores the need for clearly defined quantitative targets to enhance systematic monitoring and evaluation, ensuring full and sustainable alignment with broader European objectives.