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The Accident Emergency Warning System (AEWS) of the Danube River Basin is activated whenever there is a risk of transboundary water pollution, or threshold danger levels of certain hazardous substances are exceeded.

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.

Water quality in the Danube has improved over the years, but there is still much work to be done to meet the region’s goals for water status. To improve the water quality, an ambitious programme of measures for the whole Danube River Basin District has been agreed under the EU WFD. To assess trends in water quality, the ICPDR oversees the TransNational Monitoring Network (TNMN). The network carefully monitors physical, chemical and biological conditions in the Danube and its tributaries, and provides in TNMN Yearbooks an annual overview of pollution levels as well as long term trends for water quality in the basin.

The Black Sea Commission is an intergovernmental organisation responsible for the implementation of the Convention on the Protection of the Black Sea against Pollution, and sets the legal framework required for regional cooperation and the activities necessary to reduce pollution and enhance the protection of the marine environment.