Bogdanas river flows east of Thessaloniki in Northern Greece. Its sources are found at the western part of the Vertiskos mountain and flows along the Assiros and Lagada plane towards Koronia lake. In this study, variations of the heavy metal concentrations in Bogdanas river sediments have been evaluated. Sediment samples were collected at 8 representative sampling sites along the river, during two sampling periods. Chemical analysis indicated that the sediment samples show variable concentrations of heavy metals. Sediment quality assessment according to the limits determined by the European Community’s legislation indicated that the river sediments were not contaminated, apart from 3 samples and 1 sample concerning Zn and Cu, respectively. On the other hand, sediment quality assessment according to the US EPA Sediment Quality Guidelines (SQG) revealed that there was heavy metal pollution with respect to especially Zn, Cu and Ni. Concerning Zn, only 1 sample is close to the EPA’s moderately polluted level, while 10 samples surpass it and 5 samples exceed the EPA’s heavily polluted level. Concerning Cu, 7 samples are classified as moderately polluted and 9 samples as heavily polluted. Finally, no pollution is defined for Ni, apart from 2 samples which are classified as moderately polluted. In conclusion, the research showed that the revealed heavy metal pollution is more attributed to the lithology of the area and less to human activity.