Magmatic sources may contribute a significant amount of volatiles in geothermal springs; however, their role is poorly understood in submarine hydrothermal systems worldwide. In this study, new results of B and δ11B in 41 hydrothermal vent waters collected from the shallow hydrothermal system of Milos island in the Aegean Sea were combined with previously published data from other tectonic settings and laboratory experiments to quantify the effects of phase separation, fluid/sediment interaction and magmatic contribution. Two Cl-extreme solutions were identified, high-Cl waters (Cl as high as 2000mM) and low-Cl waters (Cl <80mM). Both sets of waters were characterized by high B/Cl (~1.2–5.3×10−3mol/mol) and extremely low δ11B (1.4–6.3‰), except for the waters with Mg content of near the seawater value and δ11B=10.3–17.4‰. These high-Cl waters with high B/Cl and low δ11B plot close to the vent waters in sediment-hosted hydrothermal system (i.e., Okinawa Trough) or fumarole condensates from on-land volcanoes, implying B addition from sediment or magmatic fluids plays an important role. This is in agreement with fluid/sediment interactions resulting in the observed B and δ11B, as well as previously reported Br/I/Cl ratios, supporting a scenario of slab-derived fluid addition with elevated B, 11B-rich, and low Br/Cl and I/Cl, which is derived from the dehydration of subducted-sediments. The slab fluid becomes subsequently mixed with the parent magma of Milos. The deep brine reservoir is partially affected by injections of magmatic fluid/gases during degassing. The results presented here are crucial for deciphering the evolution of the brine reservoirs involved in phase separation, fluid/sediment interaction and magmatic contribution in the deep reaction zone of the Milos hydrothermal system; they also have implications in the understanding of the formation of metallic vein mineralization.