The geochemical study of 5 sediment cores obtained from different shallow hydrothermal fields along the volcanic arc (Methana, Milos, Kos and Yali), revealed that the degree of rock hydrothermal alteration from one area to another is different and is influenced by the physical and geochemical properties of the hydrothermal venting fluids and the type of the rocks in the substrate. The submarine hydrothermal fields in the central Aegean Sea are linked with the Hellenic Volcanic Arc and imprint their hydrothermal influence on the local marine sediments. Hydrothermal venting fluids differ in pH, temperature, gas and metallic element content, intensity of gas and water flux, while rock substrate is variable in terms of thickness and chemistry of the marine sediments and the mineral deposits. The analytical results showed that the lowest values of Fe are observed in Palaeochori Bay (0.72%) and the highest values are found in Bros Thermi (2.72%). The highest Mn concentrations are found in Bros Thermi (407 ppm) and the lowest are found in Yali (29 ppm). Cu and Pb highest concentrations are found in Bros Thermi (21 ppm) and Thiafi Bay (16 ppm), and the lowest in Yali (1 ppm). Zn highest values are found in Bros Thermi (56 ppm) and the lowest values in Kephalos Bay (10 ppm). Finally, the Ca and Mg-richest layers are observed in Kephalos 7.5 and 0.98% respectively and the lowest are observed in Milos (0.01% for Ca) and Yali (0.12% for Mg). The hydrothermal activity presented variations with geological time and hydrothermal suspended particulate matter coming out from the vent outlets also influence the sediment geochemistry. As an example in Methana, high concentrations of Cu and Zn in SPM result in high levels of Cu and Zn in the sediments.