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The nutrient levels, notably phosphorus and nitrogen, found in the Danube River and its major tributaries hold significant international importance. This is because they directly contribute to the phenomenon of eutrophication in both the river itself and the Black Sea. Historical trend analysis of nutrient river loads over the past decades shows a significant reduction in the transported nutrient fluxes to the Black Sea. Overall nutrient emissions declined by 30% (nitrogen) and 50% (phosphorus) in the last 15 years. However, the current long-term fluxes are still considerably higher than those of the early 1960ies which represent river loads under low pressures, indicating a further load reduction potential that might be exploited for the benefit of the Black Sea. Nevertheless, in the last 5-10 years the measured loads are rather low and close to the Black Sea targets indicating significant water quality improvement.

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.