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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.

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.

The Danube and its tributaries host a variety of fascinating and diverse ecological territories with many unique plants and animals. The rich and unique biodiversity and riverine habitats have been under severe pressure due to human activities for centuries. However, today the protection of environment and biodiversity is on the political agenda of the different Danubian States.

Since the 16th century, people have been changing the natural course of the rivers in the Danube River Basin, mainly for flood defence, hydropower generation and navigation. All these changes affect the ecological quality of the rivers. Changes in the depth or width of a river typically reduce flow rates, interrupting natural sediment transportation as well as the migration routes of animals.