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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 Basin is Europe's second largest river basin, with a total area of 801,463 km². It is the world's most international river basin, flowing through the territory of 19 countries. The ecosystems of the Danube River Basin are highly valuable in environmental, economic, historical and social terms, but they are subject to increasing pressure and serious threats of pollution from agriculture, industry and cities.

Water quality in the Danube has improved over the years, but there is still much work to be done to meet the region’s goals for water status. To improve the water quality, an ambitious programme of measures for the whole Danube River Basin District has been agreed under the EU WFD. To assess trends in water quality, the ICPDR oversees the TransNational Monitoring Network (TNMN). The network carefully monitors physical, chemical and biological conditions in the Danube and its tributaries, and provides in TNMN Yearbooks an annual overview of pollution levels as well as long term trends for water quality in the basin.