This habilitation thesis synthesizes two decades of applied ecological research dedicated to the implementation of the European Water Framework Directive (WFD). It focuses on two interlinked research areas: (1) defining and harmonizing the ecological status of inland waters across Europe, and (2) understanding the effects of multiple stressors on this status. The work traces the development and intercalibration of biological assessment methods, contributing to a common ecological status classification that informs European water policy. It also addresses the complexity of co-occurring physical, chemical, and biological pressures on aquatic ecosystems, highlighting the need for systemic, cross-scale approaches in freshwater management. The thesis presents novel insights from empirical studies, modeling efforts, and conceptual frameworks that inform multiple stressor analysis and adaptive management. Extending beyond disciplinary boundaries, the work embraces post-normal science, incorporating ecosystem services and stakeholder perspectives into freshwater governance. Through extensive collaboration with EU institutions, agencies, and scientific networks, the thesis offers practical pathways to integrate robust scientific understanding into effective, value-conscious environmental policy.