Modern and past mercury (Hg) fluxes in the oceanic water column and abyssal sediments are poorly quantified. Here, we investigated the particulate transfer of Hg in the water column of the ultra-oligotrophic Ionian Sea (Eastern Mediterranean) with sediment traps during a one-year period, and its accumulation in the deep central abyssal plain using sediment cores comprising the last 10 ka. The Hg concentrations in the particles collected in the sediment traps varied from 112 to 401 ng g−1 and enabled quantifying annual Hg fluxes of 2.0, 2.5, and 2.5 μg m−2 a−1, for traps deployed at 250, 1440, and 2820 m deep, respectively. Hg collected in the upper trap originates from atmospheric deposition, including Saharan dust, which is scavenged by the biological pump. Higher Hg fluxes found at mid-depth and near-bottom than in the upper water layer are attributed to lateral advection under the mixed layer of Hg-rich resuspended sediments from the Adriatic continental margin. In the abyssal sediment, Hg concentrations range from 15 to 134 ng g−1 with the highest levels in the Sapropel S1. Methylmercury concentrations varied from 0.06 to 0.24 ng g−1 following the distribution of total Hg, with evidence of its specific accumulation at the oxidized front of the sapropel. We estimated that <1.8% of the total Hg in the sedimentary column was diagenetically reallocated. The reconstruction of historical Hg accumulation rates (HgAR) during the Holocene shows low pre-anthropogenic values (~0.3 μg m2 a−1 before 4 ka BP), increasing up to ~0.9 μg m2 a−1 during the late Iron Age and the Roman period (1.5–2.5 ka BP), and up to 2.9 μg m2 a−1 during the Industrial Era. During the Sapropel S1 period (~6–10 ka BP), HgARs rose to 6.4 μg m−2 a−1 likely due to the intensity of the Hg removal by the biological pump, the organic matter preservation, along with high inputs of Hg-rich terrigenous matter and a possible restricted recycling in the atmosphere. Hg accumulation in the Ionian Sea deep sediment is found ~3-fold lower than those in the western Mediterranean abyssal plain.