We have analysed He, Ne and CO2 concentrations and isotopic ratios in seawater samples collected using a ROV above hydrothermal fields and in CO2-accumulating pools within Santorini caldera (Greece). Our results provide new insights on the plumbing and magmatic sources of this volcano, which is critical to understand and better predict its volcanic eruptions, and its relationships to nearby volcanic systems. The 3He/4He ratio is as high as 6.54 times the atmospheric ratio, and significantly higher than any other samples from Santorini, including the active eruptive centre of Nea Kameni (~3.6 Ra). The 3He/4He ratio, corrected for atmospheric helium dissolved in seawater is ~7 Ra, a value similar to that measured at the nearby Kolumbo submarine volcano crater. The fluids display typical mantle signatures never recorded before in the active centres of the island of Santorini, in which fluids and gases are contaminated at shallow depths. The helium isotopic signature suggests that the source of volatiles for these two volcanoes is similar to the MORB source instead of being the subcontinental lithospheric mantle as suggested previously.