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The habitats created by the Danube and its tributaries host a unique mix of species. But many habitats are degraded by man-made changes to the river profile and width, water depth and flow velocity following the construction of dams, weirs and canals. Many migratory fish including sturgeon species and the Danube Salmon are endangered or close to extinction by being disconnected from their spawning grounds and habitats or by being over-exploited.

As both the largest remaining natural wetland and second largest river delta in Europe, the Danube Delta is one of the continent's most valuable habitats for wetland wildlife. Pollution and discharge manipulation from upstream has a huge effect on this area of high biodiversity, plus the delta continues to change ecologically itself – the Danube Delta spreads seaward at a rate of 10 to 25 metres every year.

A river does not end at its bank. The Danube and its tributaries form many diverse riverine habitats, including intricate networks of water bodies, creeks and channels, floodplain forests, water meadows, lakes, gravel islands, sandy banks and the unique delta habitats by the shores of the Black Sea.

The Danube and its tributaries host a variety of fascinating and diverse ecological territories with many unique plants and animals. The rich and unique biodiversity and riverine habitats have been under severe pressure due to human activities for centuries. However, today the protection of environment and biodiversity is on the political agenda of the different Danubian States.