Caesium-137 activity concentration in the water columns of the Gulf of Patras (Central Greece) and the North-Eastern Aegean Sea (easterward to Lemnos Island) was investigated in selected sampling stations during the period September 2004–June 2006. The methodology followed was based on the sorption of caesium (Cs) on cotton wound cartridge filters impregnated by Cu2[Fe(CN)6] via in-situ pumping. In terms of the horizontal and vertical records, the activity concentrations of 137Cs in the Gulf of Patras ranged between 1.2 and 6.7Bqm−3, depending on the sampling period and the prevailing physicochemical regime at the sampling station. The general pattern of the decreased activity concentrations of 137Cs with increasing depth was reversed in the Gulf of Patras during the cold period attributed to the prevailing advective processes of the area. The activity concentrations of 137Cs in the North-Eastern Aegean Sea ranged from 2.6 to 12.8Bqm−3, whereas significant stratified curves were observed during the warm period and also, in one station during the cold period. In terms of temporal variation, the discharges in the Gulf of Patras resulted in enhanced levels of 137Cs, whereas in the North Aegean Sea the incoming water masses form the Black Sea had an apparent influence throughout the year by increasing the 137Cs levels, hence presenting a weak seasonal variation. Comparing the two studied areas, one could say that the North Aegean Sea, as an open sea environment, presented higher concentrations due to the influence of the Black Sea water masses. The estimated inventories of 137Cs in the Gulf of Patras ranged 0.25±0.03–0.79±0.03kBqm−2, whereas in the North-Eastern Aegean Sea they ranged 0.33±0.02–0.92±0.03kBqm−2.