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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 habitats created by the Danube and its tributaries host a unique mix of species. But many habitats are degraded by man-made changes to the river profile and width, water depth and flow velocity following the construction of dams, weirs and canals. Many migratory fish including sturgeon species and the Danube Salmon are endangered or close to extinction by being disconnected from their spawning grounds and habitats or by being over-exploited.