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Located in the Carpathian Mountains, the Slovak Republic shares borders with Austria, the Czech Republic, Hungary, Poland and Ukraine. Water management in Slovakia is determined by its geographic position on the watershed divide between the Black and Baltic Seas. The Danube and its tributaries drain 96% of the country into the Black Sea.

The Danube begins at the confluence of the Brigach and Breg Rivers in the city of Donaueschingen located in the Black Forest, Baden-Württemberg. The German Danube catchment area covers an area of about 56,200 km²; its share of the total Danube catchment area is approx. 7%. The German Danube basin is bordered by the Rhine basin to the west and the Elbe River basin to the east.

The Danube River is seeing an influx of new non-native species, stemming from the increasing interconnections with various European and global water bodies via canals and other waterways designed to facilitate navigation. It is currently believed that alien species are very likely to become even more significant in the future, as the importance of the Danube as an international waterway increases.