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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.

Floods are natural phenomena. They can, however, turn into disasters causing widespread damage, health problems and even deaths. This is especially the case where rivers have been cut off from their natural floodplains, are confined to man-made channels, and where houses and industrial sites have been constructed in areas that are naturally liable to flooding.

The best way to protect and manage water is by close international co-operation between all the countries within the river basin – bringing together all interests upstream and downstream. All countries of the European Union are using a river basin approach for water management since the adoption of the EU Water Framework Directive.

The status of waters of the Danube River Basin is largely influenced by inputs of pollutants, particularly organic material, nutrients, hazardous substances and plastics. The ICPDR regularly updates specific emission inventories addressing both point source and diffuse emissions. The ICPDR also develops policy guidance documents providing recommendations for Danube countries on how to address pollution problems and the measures that need to be implemented in order to reduce emissions. In addition, the ICPDR supports capacity building activities on issues related to pollution control.