Three types of hydrothermal vent fluids, herein referred to as cave, submarine-brine and seawater-like, were recovered from a shallow submerged system at Milos in the Aegean Sea, Greece, for detailed chemical and isotopic analyses. The cave fluids discharge through rock fissures near sea-level and have low pH, chlorinity, and B concentrations relative to seawater. The submarine-brine fluids are characterized by high Cl and contain >10 times seawater B concentrations. A scenario involving a two-cells circulation is proposed; one occurs at 1–2 km and another at shallower depth. The deeper saline reservoir has experienced subcritical phase separation, partitioning 0.42 mM B in vapor and 6.8 mM in brine with no detectable isotopic fractionation. The reaction temperature in the saline reservoir is 313°C calculated from the Na-K-Ca geothermometry. The vapors rise directly to form the cave vents, whereas the saline fluids transport in different pathways and are influenced by seawater mixing to form the variable submarine-brine fluids. The seawater-like fluids circulate at shallower depths, where calculated temperature is 248°C and show slightly diluted B (0.36–0.41 mM) and seawater δ11B. These fluids probably resulted from heating of down-flow seawater and may have experienced groundwater discharge and partial Mg removal. This study represents the first two-cells circulation occurring at Milos and emphasizes the important role of phase separation in shallow submarine hydrothermal system.