Fluvial sediment samples (river bottom sediment, suspended sediment and active floodplain/overbank) were collected in 2 baseline stations of the Transnational Monitoring Network for each of the 12 countries in the Danube Basin Region: Austria, Bosnia and Herzegovina, Bulgaria, Croatia, Czech Republic, Hungary, Republic of Moldavia, Montenegro, Romania, Republic of Serbia, Slovakia and Slovenia, according to a harmonized methodology. The sediment samples were analyzed for selected hazardous substances (HSs):8 metals, 8 polycyclic aromatic hydrocarbons (PAHs) and 6 pesticides in an accredited laboratory selected as reference laboratory, as well as in national laboratories. Risk ratios were computed in order to compare the results to the Environmental Quality Standards listed in the European Directives, to the national threshold values in the Danube Basin, and to other available international European and American quality standards, and the risk ratios were classified as background, alert and intervention values for readily evaluation. Results show widespread metal(oid) (As, Cd, Cu, Hg, Pb, and Zn) contamination in the Danube Basin, most often associated with historic mining. Concentration values of Ni and Cr exceeding the thresholds are caused by the geological background (ultrabasic and metamorphic rocks in Bosnia and Herzegovina, Republic of Serbia and Romania).Concentration values higher than the thresholds for some of the PAHs (e.g. Fluoranthene) and sometimes for Total PAHs were also noted almost in every countries, caused by industrial activities, wastewater discharges or navigation on the Danube River. Pesticides were below the detection limit or below the legislative intervention thresholds at all national baseline sampling sites.