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The EU Water Framework Directive aims to make all waters cleaner and healthier. To meet these requirements, the ICPDR's Danube River Basin Management Plan closely examines the most important pressures affecting water status.
Significant water management issues, called SWMIs, are the central pressures of basin-wide importance affecting the ecological and chemical status of surface waters, including pollution by organic substances, nutrients, and hazardous substances, as well as hydromorphological alterations. The first interim overview on the Significant Water Management Issues was created in 2007 for the 1st DRBM. The SWMIs outlined in this report were derived based on the requirements of the WFD and mainly related to quality aspects. For transboundary groundwater bodies, both qualitative and quantitative issues are addressed.

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.