Active, shallow-water (2–10 m below sea level) and low temperature (up to 115 °C) hydrothermal venting at Paleochori Bay, nearshore Milos Island, Greece, discharges CO2 and H2S rich vapors (e.g., low-Cl fluid) and high-salinity liquids, which leads to a diverse assemblage of sulfide and alteration phases in an area of approximately 1 km2. Volcaniclastic detritus recovered from the seafloor is cemented by hydrothermal pyrite and marcasite, while semi-massive to massive pyrite-marcasite constitute mounds and chimney-like edifices. Paragenetic relationships indicate deposition of two distinct mineralogical assemblages related to the venting of high-Cl and low-Cl fluids, respectively: (1) colloform As- and Hg-bearing pyrite (Py I), associated with marcasite, calcite, and apatite, as well as (2) porous and/or massive As-rich pyrite (Py II), associated with barite, alunite/jarosite, and late-stage hydrous ferric oxides. Mercury, in the form of cinnabar, occurs within the As-rich pyrite (Py I) layers, usually forming distinct cinnabar-enriched micro-layers. Arsenic in colloform pyrite I shows a negative correlation with S indicating that As1− dominates in the pyrite structure suggesting formation from a relatively reducing As-rich fluid at conditions similar to low-sulfidation epithermal systems. On the contrary, As3+ dominates in the structure of porous to massive pyrite II suggesting deposition from a sulfate-dominated fluid with lower pH and higher fO2. Bulk sulfide data of pyrite-bearing hydrothermal precipitates also show elevated As (up to 2587 ppm) together with various epithermal-type elements, such as Sb (up to 274 ppm), Tl (up to 513 ppm), and Hg (up to 34 ppm) suggesting an epithermal nature for the hydrothermal activity at Paleochori Bay. Textural relationships indicate a contemporaneous deposition of As and Hg, which is suggested to be the result of venting from both high-salinity, liquid-dominated, as well as CO2- and H2S-rich vapor-dominated fluids that formed during fluid boiling. The CO2- and H2S-rich vapor that physically separated during fluid boiling from the high-salinity liquid led to calcite formation upon condensation in seawater together with the precipitation of As- and Hg-bearing pyrite I. This also led to the formation of sulfuric acid, thereby causing leaching and dissolution of primary iron-rich minerals in the volcaniclastic sediments, finally resulting in pyrite II precipitation in association with alunite/jarosite. The Paleochori vents contain the first documented occurrence of cinnabar on the seafloor in the Mediterranean area and provide an important link between offshore hydrothermal activity and the onshore mercury and arsenic mineralizing system on Milos Island. The results of this study therefore demonstrate that metal and metalloid precipitation in shallow-water continental arc environments is controlled by epithermal processes known from their subaerial analogues.