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The Joint Danube Survey 2001 was carried out by the ICPDR and is the most homogenous analysis of the water quality and the ecological status of the Danube River. Over 140 chemical and biological parameters were analysed and over 40.000 laboratory results were generated.

The TransNational Monitoring Network is an important tool under the Danube River Protection Convention (DRPC), whose Contracting Parties are committed to co-operate in the field of monitoring and assessment. Formally launched in 1996, the TNMN aims to provide a well-balanced overall view of pollution and long-term trends in water quality and pollution loads in the major rivers in the Danube River Basin.

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 habitats created by the Danube and its tributaries host a unique mix of species. But many habitats are degraded by man-made changes to the river profile and width, water depth and flow velocity following the construction of dams, weirs and canals. Many migratory fish including sturgeon species and the Danube Salmon are endangered or close to extinction by being disconnected from their spawning grounds and habitats or by being over-exploited.

A river does not end at its bank. The Danube and its tributaries form many diverse riverine habitats, including intricate networks of water bodies, creeks and channels, floodplain forests, water meadows, lakes, gravel islands, sandy banks and the unique delta habitats by the shores of the Black Sea.