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Moldova is one of the smaller countries of the Danube River Basin, but the Danube touches the southern point of Moldova for about 340 meters. Picturesque Moldova holds over 12,500km² of the Danube River Basin, including 8,300km² of the Prut River Sub-Basin, 3,300km² of the Yalpugh River Sub-Basin and 900km² of the Cahul River Sub-Basin.

The Danube begins at the confluence of the Brigach and Breg Rivers in the city of Donaueschingen located in the Black Forest, Baden-Württemberg. The German Danube catchment area covers an area of about 56,200 km²; its share of the total Danube catchment area is approx. 7%. The German Danube basin is bordered by the Rhine basin to the west and the Elbe River basin to the east.

Organic pollution has been on the rise in the Danube over the last century, as human activities have resulted in increasing loads of wastewater rich in organic matter. The most serious organic pollution problems occur in tributaries that regularly receive untreated or inadequately treated wastewater from industrial plants and municipalities. Thanks to the significant improvement of wastewater infrastructure and services in the Danube countries, the basin-wide organic emissions reduced by 60% since the mid 2000s.

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.