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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.

The Danube River Basin is Europe's second largest river basin, with a total area of 801,463 km². It is the world's most international river basin, flowing through the territory of 19 countries. The ecosystems of the Danube River Basin are highly valuable in environmental, economic, historical and social terms, but they are subject to increasing pressure and serious threats of pollution from agriculture, industry and cities.