The Danube River is known for its rich biodiversity resulting from the coupled evolution of specific natural and cultural characteristics. The Danube delta, for instance, is the largest remaining natural wetland in Europe. It is inhabited by 5,000 animal and plant species, many of which are endangered or close to extinction. Preserving and restoring this natural heritage often gets in conflict with traditional societal practices and future requirements. So far, compromise solutions are often lacking. At the same time legacies from the distant and recent past contribute to present environmental problems such as pollution or hydromorphological alterations. This paper presents examples for the long-term history of both natural heritage and environmental legacies, and discusses approaches to biodiversity conservation against the background of climate change