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Sturgeons are sensitive to environmental pressures and therefore valuable indicators for healthy rivers. This is why the ICPDR has endorsed sturgeons as flagship species. There are six species of sturgeons native in the Danube River Basin, but the survival of these ancient fish is threatened by a range of issues. Through the "Danube Sturgeon Task Force", the ICPDR contributes to actions such as the protection of habitats, the development of migration aids, the breeding of healthy stocks in sheltered facilities, or the struggle against illegal fishing and caviar trade.

The key purpose of Joint Danube Surveys (JDS) is to produce reliable and comparable information on carefully selected elements of water quality for the length of the Danube River, including its major tributaries. Three Joint Danube Surveys have previously been conducted, in 2001, 2007, 2013, and 2019. The 5th Joint Danube Survey is due to launch on 1st July 2025.

Groundwater constitutes the largest reservoir of freshwater in the world, accounting for over 97% of all freshwaters available on earth (excluding glaciers and ice caps). The remaining 3% is composed mainly of surface water (lakes, rivers, wetlands) and soil moisture. By incorporation into the Water Framework Directive (WFD), groundwater became part of an integrated water management system.

JDS 2, the world's biggest river research expedition, was held in 2007. Its goal was to produce comparable and reliable information on water quality and pollution for the Danube and some tributaries. The ICPDR coordinated its implementation. Launched on August 14, 2007 in Germany, three JDS2 boats traveled downstream the Danube, through 10 countries, to the Danube Delta.

The investigation of the Tisza River was a follow-up project of the Joint Danube Survey 2001 organised by the ICPDR. The objective of the survey was to investigate the water quality along the river and to promote public awareness. The countries participating at the survey include Romania, Slovakia, Hungary, and Serbia and Montenegro.

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.

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.

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.