The study analyzes the presence and the origin of heavy metals in environmental compartments affected by anthropogenic activities. The paper presents the results of a field study performed on the sediments of two of the main small urban creeks of the city of Prague (Czech Republic). The aim of the survey was to verify the presence and bioavailability of heavy metals (Cu, Cr, Ni, Pb, Zn) in the aquatic environment (water as well as bottom sediments), and to assess the source of these pollutants. The results were processed to evaluate the enrichment factor and the partition coefficient, and were statistically analyzed through the analysis of variance and the principal component analysis. Comparison with relevant environmental quality standards showed that measured heavy metal concentrations were always lower than the probable effect concentration (PEC). On the contrary, the threshold effect concentration (TEC) was frequently exceeded. Sequential extraction analysis showed that the bioavailability of studied metals is quite high, suggesting that they could be easily released from the sediment to the aquatic environment. Overall, several sources of pollution, different for the different metals, were identified, all related with anthropogenic factors.