Utilizing the sequential extraction procedure (acid soluble, reducible, oxidizable, and residual) proposed by The European Community Bureau of Reference (BCR), the trace metals present in the sediments of the Ergene River, Turkey, were determined. The sediment samples were collected from 10 sampling sites and analyzed to identify the concentrations of cadmium, cobalt, chromium, copper, manganese, nickel, lead and zinc. The flame atomic absorption spectrometer was used for metal determination. The validation of the results was checked by the analysis of the BCR-701 standard reference material. The relationship existing between the sediment characteristics and metal fractions was identified using the correlation analysis. Hierarchical cluster analysis was performed to find out the grouping of the sampling sites based on the similarities of the heavy metals in the bioavailable fraction. When the extractable amounts of heavy metals are considered, the quantity of the mobile fractions (viz., acid soluble, reducible, and oxidizable) of the heavy metals is observed to be higher when compared with that of the immobile fraction (residual). This might be caused by the anthropogenic sources. Besides, it was statistically discovered that the organic matter, pH and clay contents could influence the bonding of the analyte metals in various forms. The cluster analysis revealed three clusters of the sampling stations, with group I (S5-8) and group II (S3, S4 and S9) showing higher environmental risks. The risk assessment code indicated that the highly mobile soluble fractions of Mn, Zn, Cd and Co created a high environmental risk which could result in negative impacts on the aquatic biota.