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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.

daNUbs was a mulitnational EU research project carried out under the leadership of the Technical University of Vienna. The results from this project include estimates of nutrient inputs into the river network (MONERIS), as well as an assessment of the loads of nitrogen, phosphorus and silica transported via the river network. These results indicate that the nutrient status in the Black Sea has significantly improved since the 1980s.

The Accident Emergency Warning System (AEWS) of the Danube River Basin is activated whenever there is a risk of transboundary water pollution, or threshold danger levels of certain hazardous substances are exceeded.

Accidental pollution in the Danube River Basin can cause widespread damage to the environment, and endanger the health of local people and the state of local economies downstream. This was exemplified by the effects of the Baia Mare cyanide spill in Romania in 2000 or by the Hungarian redsludge accident at Ajka in 2010. The ICPDR is working to prevent accidental pollution and to improve response capability by compiling an inventory of all relevant "Accident Risk Spots".

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.

Hazardous substances can remain in the environment for a very long time, and harm ecosystems and human health. Although monitoring indicates that the loads of some substances have been reduced in recent years, many problems still persist. The increasing number of these man-made substances present in the environment is a matter of concern, and calls for the application of the precautionary principle.

The nutrient levels, notably phosphorus and nitrogen, found in the Danube River and its major tributaries hold significant international importance. This is because they directly contribute to the phenomenon of eutrophication in both the river itself and the Black Sea. Historical trend analysis of nutrient river loads over the past decades shows a significant reduction in the transported nutrient fluxes to the Black Sea. Overall nutrient emissions declined by 30% (nitrogen) and 50% (phosphorus) in the last 15 years. However, the current long-term fluxes are still considerably higher than those of the early 1960ies which represent river loads under low pressures, indicating a further load reduction potential that might be exploited for the benefit of the Black Sea. Nevertheless, in the last 5-10 years the measured loads are rather low and close to the Black Sea targets indicating significant water quality improvement.

The floodplains and wetlands of the Danube basin are uniquely valuable ecosystems in global terms, although few areas are still in their natural or near-natural state.

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.