The Carpathians and the Alps belong to the most important natural areas in Europe. The designation of the Alpine-Carpathian Corridor ensured that the ecological link between these large areas is guaranteed. Habitat connectivity for aquatic organisms in the Austrian-Slovakian border region should also now be protected and improved within the framework of the Alpine Carpathian River Corridor. The large protected areas (Donau-Auen, Zahorie, Wienerwald, Morava) in the metropolitan area of Vienna-Bratislava are of outstanding importance for nature conservation and local recreation. However, they can only achieve their protection goals if they remain connected through habitat corridors. The network of waterways plays an important role in this protection. Regulations, transversal structures, weak structure of Low Riparian Forests and intensive agriculture in the surrounding area affect their multi-functionality. Cross-border protection and care concepts for selected rivers (Rudava, Malina, Myjava, Mociarka in Slovakia, Schwechat and Fischa in Austria) are being developed jointly by experts from both countries. Pilot revitalization measures improve the habitat quality of the rivers and contribute to flood protection in the region. The success of the implemented project measures is documented based on selected species (Kingfisher, Common Nase, Dice Snake, Ukrainian Brook Lamprey). The involvement of neighboring communities, interested parties and schools in the project activities should make the rivers in the Austrian-Slovak border region more tangible again and rekindle the enthusiasm for the river habitat.