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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 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.

The Danube River Protection Convention forms the overall legal instrument for co-operation on transboundary water management in the Danube River Basin. The Convention was signed on June 29 1994 in Sofia (Bulgaria) and came into force in 1998. It aims to ensure that surface waters and groundwater within the Danube River Basin are managed and used sustainably and equitably.