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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.

Despite the EU's advanced waste management and ambitious recycling objectives, studies still indicate the presence of macro and microplastic pollution in EU rivers. The Tid(y)Up project focuses on improving water quality and reducing plastic pollution in the Tisza River, which is long considered one of Europe’s most heavily contaminated rivers.

The project aims to restore the Danube River Basin for ecosystems and people, an EU ‘Lighthouse Initiative’ supporting the Mission to “Restore our ocean and waters by 2030."Launched in January 2023, DANUBE4all is a 5-year EU "Lighthouse Initiative" project funded by Horizon Europe, aiming to restore freshwater ecosystems in the Danube River Basin.

Rivers, lakes, transitional and coastal waters, as well as groundwater, are vital natural resources. A significant proportion of water resources are exposed to environmental pollution or other potentially damaging pressures. Protecting and improving the waters of the Danube River Basin is therefore essential for the natural environment, the sustainable development of the region and the long-term health, well-being, and prosperity of the population.

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.

On 18 October 2022, the Central and Eastern Europe WWF participated in a side event on “Achieving Functional Biodiversity in the Danube-Carpathian Region by Mainstreaming Ecological Connectivity – how to make it happen” during the 11th EUSDR Annual Forum 2022. The annual forum, which took place in a hybrid format, was jointly organized by the Ukrainian EUSDR Presidency, the former Slovak EUSDR Presidency, the European Commission, and the Danube Strategy Point, with the financial support of the Danube Transnational Programme.