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This paper examines the role of transnational cooperation in conserving the ecological integrity of the Danube River through the DANUBEPARKS network of protected areas. As Europe’s most species-rich river system, the Danube connects diverse biogeographic regions, yet faces increasing pressure from habitat degradation, pollution and hydrological modifications. Recognizing the need for a unified approach, protected area administrations across the basin have formed partnerships to address shared conservation challenges. The paper traces the evolution of this collaboration from early bilateral agreements to the establishment of the DANUBEPARKS Association, a network fostering ecological connectivity and coordinated restoration. A key achievement is the development of the WILDisland concept, which identifies islands as critical habitats and indicators of riparian ecosystem health. Additionally, the network’s advocacy efforts have contributed to the formation of the Danube WILDisland Ramsar Regional Initiative, securing international recognition and policy support for long-term conservation. By bridging protected areas and aligning conservation goals across borders, DANUBEPARKS Association serves as a model for integrated river basin management. Its success demonstrates the power of trust, shared governance and cross-sector partnerships in overcoming political, economic and ecological barriers ensuring the sustainable management of one of Europe’s most vital waterways. Cross-country cooperation facilitates efficient conservation of shared natural resources. Common conservation goals unite and drive joint action across the Danube. Bottom-up initiatives evolve into sustainable structures for transnational governance. The WILDisland concept promotes islands as key habitats for river ecosystem health.