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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.

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.

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.