Surficial and sub-surficial sediments obtained from the lower course of the Kifissos River, which drains the Athens Basin, have been analyzed for heavy metals and aliphatic and polycyclic hydrocarbons. Oddly, the calculated enrichment factors for the identified heavy metals, with the baseline taken from a pristine area in the adjacent Saronikos Gulf, are very low excluding only those related to Cu and Zn. In contrast, the enrichment factors for the measured hydrocarbons are particularly high. However, physicochemical water conditions and annual flushing episodes of the Kifissos River may have reduced significantly the sediment chemical fingerprint found out by the present study. Moreover, an evaluation of the fluvial sediment quality based on the enriched Cu and Zn amounts and concentration of PAH fraction with a consideration of the biological thresholds proposed by the National Oceanic and Atmospheric Administration (USA) reveals little probability for serious biological impairments. Additionally, sediment toxicity due to the sediment PAH load may be considered as minimum.