Seafloor hydrothermal activity may constitute a considerable mercury (Hg) source to the oceans, but the flux from marine shallow-water hydrothermal systems (MSWHS) remains poorly constrained to date. To study the presence of Hg in MSWHS in Paleochori Bay (Milos Island, Greece), sea surface, bottom, pore fluid and hydrothermal gas samples were collected in June of 2017, October of 2018 and July of 2020, and analyzed for Cl, Br, SO4, As, Ca, Fe, K, Mg, Mn, Na, Si, Sr, H2S, unfiltered total Hg (THg), and filtered Hg (Hgdiss). Specific sites were selected for the analysis of volatile elemental Hg (Hgo), dimethylmercury (DMHg), monomethylmercury (MMHg), and Hg in the gas phase (Hggas). Concentrations of THg observed in samples collected from the sea surface were elevated compared to surface samples taken outside Paleochori Bay. The highest surface water concentrations (~10 to 15 pM) were measured in samples collected directly above shallow-water hydrothermal discharge areas. Pore fluids outside Paleochori Bay were significantly lower in THg (0.8 to 8.6 pM) than those taken inside (17.4 to 1511 pM). Porewaters collected from areas with visible gaseous or fluid emission were highly variable but generally elevated in THg concentrations (185 to 5066 pM). Concentrations within gases ranged from 0.7 to 2791 nmol/m3. The vast majority of samples with highly elevated THg (> 100 pM) had low Na/K ratios (< 15), indicative of rapidly rising fluid. Concentrations of Hg0, DMHg, and MMHg were below detection limits in all samples.Bottom substrate type (e.g., rocky vs. sediment covered) likely affected infiltration rates of oxygenated seawater below the sediment-water interface, thereby affecting Hg speciation and removal by precipitation. Flux rates from porewaters compared to those with gaseous emission were high (12.56 to 1088 mol THg/year and 0.37 to 1.85 mol THg/year). Sites with slow gaseous emission rates are hypothesized to have extended subsurface reaction times, resulting in lower Hg concentrations emitted to bottom waters. However, increasing rates of gas emission did not necessarily indicate higher Hg concentrations. The scavenging of Hg in the sediments and advective flux out of Paleochori Bay likely prevent significant accumulations of THg in the water column of Paleochori Bay. The total atmospheric flux from Paleochori Bay using average flux calculations over the entire surface area would contribute 6 mmol Hg/year to the atmosphere.We hypothesize that Hg concentrations within the pore fluids of Paleochori Bay reflect a balance between mixing and precipitation in the subsurface. A three-component mixing system of vapor, brine and seawater determines THg concentrations; however, precipitation due to sulfur cycling, changes in redox conditions and temperature, all play a crucial role in removing Hg from emitted fluids and gases.