<p>The biogeochemical dynamics of <i>Hg</i>, and specifically of its three species <i>Hg</i><sup>0</sup>, <i>Hg</i><sup><i>II</i></sup>, and <i>MeHg</i> (elemental, inorganic, and organic, respectively) in the marine coastal area of Augusta Bay (southern Italy) have been explored by the high resolution 3D Hg (HR3DHG) model, namely an advection-diffusion-reaction model for the dissolved mercury in the seawater compartment coupled with i) a diffusion-reaction model for dissolved mercury in the pore water of sediments and ii) a sorption/de-sorption model for total mercury in the sediments. The spatio-temporal variability of dissolved and total mercury concentration both in seawater ([<i>Hg</i><sub><i>D</i></sub>] and [<i>Hg</i><sub><i>T</i></sub>]) first layers of bottom sediments ([<i>Hg</i><sup><i>sed</i></sup><sub><i>D</i></sub>] and [<i>Hg</i><sup><i>sed</i></sup><sub><i>T</i></sub>]), and the <i>Hg</i> fluxes at the boundaries of the 3D model domain have been theoretically reproduced, showing an excellent agreement with the experimental data, collected in multiple field observations during six different oceanographic cruises. The mass-balance of the different <i>Hg</i> species in seawater has been calculated for the Augusta Harbor, improving previous estimations. The HR3DHG model includes modules that can be implemented for specific and detailed exploration of the effects of climate change on the spatio-temporal distribution of <i>Hg</i> in highly contaminated coastal-marine areas.</p>