The objective of this study was to assess the concentration levels of trace metals (Zn, Hg, Cd, Cr, Ni, Pb and Cu) in surface water and bottom sediments of the Hungarian upper section of the Danube River and its main tributaries. A total of 935 samples (water and sediments) were collected from 10 different sampling sites in the period of 2001–2012 and analyzed for the trace metals. Moreover, the dissolved arsenic content was determined in a number of 467 water samples in the period of 2004–2012. The highest dissolved trace element concentrations were observed at the site of Kenyérmezei-patak Creek located near a hazardous waste incinerator. However, the comparison of the dissolved trace metal(loid) concentrations determined with other sections of the Danube River and the European Union environmental quality standards revealed that the dissolved trace metal(loid) concentrations were relatively low in the Hungarian upper section during the 12-year study period (excluding some samples for Hg, Cd and Cr). The concentrations of trace metals in sediments were higher than those found in water samples and varied very much in all sampling sites during the study period. The sediment samples were mainly classified as low or moderate polluted for trace metals. However, some sediment samples collected especially from the Moson Danube branch indicated a considerable (for Zn, Hg, Cd, Ni and Cu) or a very high (for Zn and Hg) contamination.