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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 floodplains and wetlands of the Danube basin are uniquely valuable ecosystems in global terms, although few areas are still in their natural or near-natural state.

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.

Since the 16th century, people have been changing the natural course of the rivers in the Danube River Basin, mainly for flood defence, hydropower generation and navigation. All these changes affect the ecological quality of the rivers. Changes in the depth or width of a river typically reduce flow rates, interrupting natural sediment transportation as well as the migration routes of animals.