Marginal seas are directly subjected to anthropogenic and natural influences from land in addition to receiving inputs from the atmosphere and open ocean. Together these lead to pronounced gradients and strong dynamic changes. However, in the case of mercury emissions from these seas, estimates often fail to adequately account for the spatial and temporal variability of the elemental mercury concentration in surface water (Hg⁰_wat). In this study, a method to measure Hg⁰_wat at high resolution was devised and subsequently validated. The better-resolved Hg⁰_wat dataset, consisting of about one measurement per nautical mile, yielded insight into the sea's small-scale variability and thus improved the quantification of the sea's Hg⁰ emission. This is important because global marine Hg⁰ emissions constitute a major source of atmospheric mercury. Research campaigns in the Baltic Sea were carried out between 2011 and 2015 during which Hg⁰ both in surface water and in ambient air were measured. For the former, two types of equilibrators were used. A membrane equilibrator enabled continuous equilibration and a bottle equilibrator assured that equilibrium was reached for validation. The measurements were combined with data obtained in the Baltic Sea in 2006 from a bottle equilibrator only. The Hg⁰ sea–air flux was newly calculated with the combined dataset based on current knowledge of the Hg⁰ Schmidt number, Henry's law constant, and a widely used gas exchange transfer velocity parameterization. By using a newly developed pump–CTD with increased pumping capability in the Hg⁰ equilibrator measurements, Hg⁰_wat could also be characterized in deeper water layers. A process study carried out near the Swedish island Øland in August 2015 showed that the upwelling of Hg⁰-depleted water contributed to Hg⁰ emissions of the Baltic Sea. However, a delay of a few days after contact between the upwelled water and light was apparently necessary before the biotic and abiotic transformations of ionic to volatile Hg⁰ produced a distinct sea–air Hg⁰ concentration gradient. This study clearly showed spatial, seasonal, and interannual variability in the Hg⁰ sea–air flux of the Baltic Sea. The average annual Hg⁰ emission was 0.90 ± 0.18 Mg for the Baltic proper and extrapolated to 1.73 ± 0.32 Mg for the entire Baltic Sea, which is about half the amount entrained by atmospheric deposition. A comparison of our results with the Hg⁰ sea–air fluxes determined in the Mediterranean Sea and in marginal seas in East Asia were to some extent similar but they partly differed in terms of the deviations in the amount and seasonality of the flux.