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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.

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.

The status of waters of the Danube River Basin is largely influenced by inputs of pollutants, particularly organic material, nutrients, hazardous substances and plastics. The ICPDR regularly updates specific emission inventories addressing both point source and diffuse emissions. The ICPDR also develops policy guidance documents providing recommendations for Danube countries on how to address pollution problems and the measures that need to be implemented in order to reduce emissions. In addition, the ICPDR supports capacity building activities on issues related to pollution control.