Seventy-eight and three hundred and twenty-four seawater samples collected from Black Sea and North Aegean Sea respectively were analysed for dissolved trace elements. The trace element concentrations in the region near the Danube Delta, which is further influenced by the polluted waters of the Rivers Dnieper and Dniester, vary from 0.36 to 13.7 nM for Cd, from 4.7 to 36.2 nM for Cu and from not detected levels to 29.1 nM for Mn. In general, trace element levels in the Black Sea are higher than in the North Aegean. The latter reflect trace metal concentrations similar to those of the Mediterranean Sea. The concentrations in the North Aegean Sea vary from 0.022 to 0.420 nM for Cd, from 0.74 to 5.93 nM for Cu, from 2.22 to 8.46 nM for Ni and from 0.07 to 44.98 for Mn. There is a strong evidence that Black Sea water influences the surface waters of the North Aegean Sea. Hence, surface concentrations recorded for Cd, Cu, Ni and Mn are enhanced when compared with the deeper water layers. Manganese concentrations in the upper layer (0–50 m) were found one order of magnitude higher than those of the rest of the water column in the area first receiving Black Sea water.