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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.

A recent large-scale modelling study has shown that restoring floodplains and reconnecting cut-off water bodies with the Danube River, and its tributaries could play a significant role in improving water quality and removing nitrate pollution in the Danube River Basin.