Chemical composition data for the Danube River and its tributaries sediments were analyzed using positive matrix factorization (PMF). The objective was to identify both natural and anthropogenic sources affecting Danube Basin. During the Joint Danube Survey 2 (JDS2) campaign 148 bottom sediments samples were collected. The following elements were analyzed using the X-ray fluorescence technique: Al, As, Ca, Cd, Cl, Co, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, Pb, S, Si, Ti, V and Zn. Mercury was determined by cold vapour atomic absorption spectrometry. Three factors were obtained considering the whole dataset (Danube and tributaries), identified as: (i) carbonate component characterized by Ca and Mg; (ii) alumino-silicate component dominated by Si and Al content and the presence of some metals attributed to natural processes; (iii) anthropogenic source identified by Hg, S, P and some heavy metals load. To better characterize the role of tributaries, the Danube and tributaries datasets, were also analyzed separately. The same three factor structures were identified in the Danube dataset. For the tributaries, a four-factor source model gave one further factor dominated by S and P, which could be attributed to the use of fertilizers in agriculture.