Estuaries play a vital role in the coastal environment by filtering pollutants and nutrients from catchment runoff. In areas where acid sulfate (AS) soils are abundant, the importance of the estuary as a coastal filter is heightened as AS soils typically stress the marine environment with acidic metal-laden drainage waters. In this study, we took sediment cores from a shallow estuary in Western Finland and used geochemical and palaeoecological methods to investigate how the estuary is affected by loading from AS soils. An overall decrease in diatom species richness and diversity in the estuarine sediments was found, with a clear change from species preferring pelagic conditions to species indicative of more eutrophic conditions. The change coincides with human disturbance during the early 20th century when extensive drainage and rework of forests and peatlands into agricultural use increased. Geochemical analyses show a significant enrichment of Cd, Ni, Co, Zn and Al in the estuarine sediments which correspond to the metal loads originating from the catchment AS soils. Our calculations, however, show that in comparison to the total load of soluble metals from the catchment area, more than 80% of chalcophiles and 70% of Al are transported further out to sea. We hypothesised that a precipitation gradient driven by changes in pH and salinity due to seawater mixing would form along a transect towards the estuary outlet. Instead, we found that physical sedimentation processes are stronger drivers for element transport, as enrichment takes place only in low-energy hydrodynamic conditions at greater water depths. Glacioisostatic land uplift and significant particle transport from the catchment area are further isolating the estuary, effectively moving the saline gradient seawards and diminishing the role of the estuary as a coastal filter. We also found that the estuarine sediments are hypersulfidic and contain stores of potential acidity significantly larger than conventional AS soils. Without proper management, disturbance of the estuarine sediments can cause disastrous consequences at a local level.