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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.

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.

The waters of Bosnia and Herzegovina are split between the Danube River Basin District and the Adriatic Sea Basin. Some 40.2% of the Sava river sub-basin, the second largest sub-basin of the Danube River Basin, lies in Bosnia and Herzegovina. The rest of the watershed is shared by Croatia, Serbia and Slovenia.

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.

The Sava is the Danube's largest tributary of the Danube in terms of discharge and the second largest in terms of catchment area. The Sava is shared by Slovenia, Croatia, Bosnia and Herzegovina, Serbia and Montenegro. The joint management arrangements acted as a pilot for the implementation of the European Union's Water Framework Directive for the Danube and Europe.

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.

Many people consider droughts to be rare, but in fact they are a normal and recurrent feature of the climate. Drought events are regional phenomena, affecting transnational water management. Unfortunately, droughts have a high damage potential: economic losses, ecological damages, and implications on human health.

Historically, the Danube and some of its tributaries have formed important trade routes across Europe. The harnessing of these rivers to facilitate navigation has radically changed their physical and ecological characteristics, while pollution from ships and boats is also a significant problem. In order to address this problem, the ICPDR is undertaking various activities.

Agriculture has long been a major source of income for many people living in the Danube River Basin. Today however, it is also a major source of pollutants – including fertilizers and pesticides and facing emerging issues like water scarcity and droughts.