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Current knowledge of long-term mercury (Hg) deposition is predominantly based on studies from the Northern Hemisphere, leading to a geographical bias in the comprehension of the global Hg cycle. Aiming to contribute to fill this knowledge gap, our study presents a high-resolution Hg record of a seagrass Posidonia australis sedimentary archive encompassing the last 3300 years in the Waychinicup estuary (Western Australia, WA). This setting is an ideal site for studying the natural Hg cycle, as it is located in the southwest of the state, outside the prevailing wind patterns that transport emissions from major Hg sources. Our results show that Hg concentrations fluctuated from ∼1300 BCE to 100 CE with a shift in the paleorecord around 350 BCE, which could potentially be associated with an intensified El Niño Southern Oscillation period. From around 100 until ∼1880 CE, the Hg concentration remained relatively constant (∼2 μg kg−1) with an increase up to 8 μg kg−1 from 1880 CE until present. Although Hg accumulation doubled since European settlement in WA (from 2.4 to 4.8 μg m−2 yr−1), such an increase can be explained by enhanced organic carbon accumulation, rather than changes in external Hg fluxes. Therefore, our study showcases the importance of considering biogeochemical processes when reconstructing long-term Hg accumulation based on sedimentary archives. Furthermore, the results demonstrate the key role of seagrass meadows as natural paleoarchives of environmental contamination, providing valuable insights into human impacts on coastal areas and to establish pre-anthropogenic baseline metal concentrations.