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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.

Covering an area of 157,186 km², the Tisza River Basin is the largest sub-basin of the Danube River Basin. The Tisza River is the longest tributary of the Danube (966 km), and second largest in terms of flow after the Sava. The countries of the Tisza Basin (Ukraine, Romania, Hungary, Slovakia, Serbia) agreed to close transboundary co-operation, aiming to achieve integrated water resources management of the Basin.

The Drava River is the fourth largest, as well as the fourth longest Danube tributary. It connects the Alps with the Danube and the Black Sea. The Drava has been considerably regulated with dams constructed to generate hydroelectricity and channels dredged to direct its flow. Nevertheless, natural habitats along the middle and lower reaches host unique varieties of flora and fauna, and several endemic species.