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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.

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.

The Danube River Protection Convention forms the overall legal instrument for co-operation on transboundary water management in the Danube River Basin. The Convention was signed on June 29 1994 in Sofia (Bulgaria) and came into force in 1998. It aims to ensure that surface waters and groundwater within the Danube River Basin are managed and used sustainably and equitably.