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With a national territory of 87,609 km2, Croatia is at the intersection of the Pannonian Plain, the Balkans and the Adriatic. The country straddles the border of two major catchment areas: the Danube Basin and the Adriatic Sea. Draining over 62% of Croatia’s mainland, the Danube Basin covers the northern and central inland section of the country and is home to 69% of the population. Croatian territory accounts for 4.4% of the entire Danube Basin.

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.