This study examines the concentrations of Pd, Cu, Zn and Cd in two large Greek harbours located in the Aegean Sea; these are: the harbour of the city of Heraklion (Southern Aegean, Cretan Sea) and the harbour of the city of Alexandroupoli (NE coast of the Aegean Sea).The harbour of Heraklion city is located in the northern continental shelf of the island of Crete, which is very narrow (<2km) and relatively steep sloping. The harbour of Alexandroupolis has a length of 2km and it is located in the homonymous Gulf which belongs to the inner continental shelf of the NE Aegean (Samothraki Plateau). The present contribution is based on thirteen and eleven samples recovered from the surrounding area of the Heraklion and Alexandroupolis harbour, respectively. The concentrations of the metals (Pd, Cu, Zn and Cd) have been determined with the use of the method of atomic absorption, whilst the enrichment factor has been calculated according to the standard values for the Mediterranean Sea, proposed by the World Health Organization (WHO, 1995). The concentration of Cu in Heraklion harbour varies in between 13.65 and 70.31 ppm, slightly higher than those of Alexandroupolis harbour, where they vary from 6.9 to 69.9 ppm. Pb and Cd in Alexandroupolis present relatively higher values (Pb: 13.5-107.1, Cd: 0.08-1.47) compared to the Heraklion (Pb: 10.42-63.0 ppm and Cd: 0.8-14.7 ppm). Zn concentrations in Alexandroupoli, ranging from 55.8 to 172.0 ppm, are much higher than those of Heraklion (29.6-125.3 ppm). In both coastal areas the environmental impact of the harbours can be identified as in most of the stations the enrichment factor is greater than 1 and for all metals except Pb. However, they cannot be characterized as highly contaminated areas. This is in accordance to the hydrodynamic conditions that favour the mobility of the sea bed sediments.