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The ICPDR supports the active involvement of stakeholders and civil society on all levels of its work. Two of the most important plans to the ICPDR are the Danube River Basin Management Plan and the Flood Risk Management Plan, aiming to implement the legal requirements of Water Framework Directive (WFD) and the Floods Directive (FD), comprising strategic guiding plans for water management over the course of six years. Both are to be updated with a range of public consultation measures.

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 is seeing an influx of new non-native species, stemming from the increasing interconnections with various European and global water bodies via canals and other waterways designed to facilitate navigation. It is currently believed that alien species are very likely to become even more significant in the future, as the importance of the Danube as an international waterway increases.