Sediment is an essential and dynamic part of our river basins. As surface-water flow rates decline in lowland area, transported sediment settles along the river and banks by sedimentation. Water body sediments and their characterization from viewpoint of microelements and especially heavy metals and potentially hazardous substances represent an important ecosystem and indicator of environmental quality assessment of the long-term significance. Memory effect, mainly in dated sediment cores as historical records reflect variations of pollution intensities in a catchments area. In order to comply with the Directive 76/464/EEC of the EU that requires monitoring of persistent, toxic and bio-accumulated substances commonly designated as hazardous substances, the samples of water, sediment and biota from the Danube River and its main tributaries Sava, Tisza, Velika Morava and Pek were investigated [1]. Samples were collected from 3 to 18 July 2002 at 17 localities (32 sampling points). This work presents the results for petroleum hydrocarbons in bottom sediments in the Danube and Sava rivers. The results indicate that in mouth area of the Sava River located in lowland on the both river sides the concentrations of petroleum hydrocarbons are higher than Target value (50 mg/kg) but less than intervent value (5000 mg/kg) according to the Dutch legislative [2]. The concentrations ranged between 170 and 842 mg/kg in dried sediment and increased with the depth. Same situation is in sediments along the Danube River. Concentrations of petroleum hydrocarbons are between 98 and 1340 mg/kg in dried sediment.