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Accidental pollution in the Danube River Basin can cause widespread damage to the environment, and endanger the health of local people and the state of local economies downstream. This was exemplified by the effects of the Baia Mare cyanide spill in Romania in 2000 or by the Hungarian redsludge accident at Ajka in 2010. The ICPDR is working to prevent accidental pollution and to improve response capability by compiling an inventory of all relevant "Accident Risk Spots".

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.

Floods are natural phenomena. They can, however, turn into disasters causing widespread damage, health problems and even deaths. This is especially the case where rivers have been cut off from their natural floodplains, are confined to man-made channels, and where houses and industrial sites have been constructed in areas that are naturally liable to flooding.

The best way to protect and manage water is by close international co-operation between all the countries within the river basin – bringing together all interests upstream and downstream. All countries of the European Union are using a river basin approach for water management since the adoption of the EU Water Framework Directive.