As critical transition zones between the land and the sea, estuaries are not only hotspots of hydrogeochemical and microbial processes/reactions, but also play a vital role in processing and transferring terrestrial fluxes of metals and nutrients to the sea. This study focused on three estuaries in the Gulf of Bothnia. All of them experience frequent inputs of acidic and Mn/metal-rich creek waters due to flushing of acid sulfate soils that are widespread in the creekś catchments. Analyzing existing long-termwaterchemistrydata revealed a strong seasonal variation of Mn loads, with the highest values in spring (after snow melt) and autumn (after heavy rains). We sampled surface waters, suspended particulate matter (SPM), and sediments from the estuarine mixing zones and determined the loads and solid-phase speciation of Mn as well as the composition and metabolic potentials of microbial communities. The results showed that the removal, cycling, and lateral transport of Mn were governed by similar phases and processes in the three estuaries. Manganese X-ray absorption spectroscopy data of the SPM suggested that the removal of Mn was regulated by silicates (e.g., biotite), organically complexed Mn(II), and MnOx (dominated by groutite and phyllomanganates). While the fractional amounts of silicate-bound Mn(II) were overall low and constant throughout the estuaries, MnOx was strongly correlated with the Mn loadings of the SPM and thus the main vector for the removal of Mn in the central and outer parts of the estuaries, along with organically complexed Mn(II). Down estuary, both the fractional amounts and average Mn oxidation state of the MnOx phases increased with (i) the total Mn loads on the SPM samples and (ii) the relative abundances of several potential Mn-oxidizing bacteria (Flavobacterium, Caulobacter, Mycobacterium, and Pedobacter) in the surface waters. These features collectively suggested that the oxidation of Mn, probably mediated by the potential Mn-oxidizing microorganisms, became more extensive and complete towards the central and outer parts of the estuaries. At two sites in the central parts of one estuary, abundant phyllomanganates occurred in the surface sediments, but were converted to surface-sorbed Mn(II) phases at deeper layers (>3–4 cm). The occurrence of phyllomanganates may have suppressed the reduction of sulfate in the surface sediments, pushing down the methane sulfate transition zone that is typically shallow in estuarine sediments. At the outermost site in the estuary, deposited MnOx were reduced immediately at the water–sediment interface and converted most likely to Mn carbonate. The mobile Mn species produced by the Mn reduction processes (e.g., aqueous Mn(II) and ligand complexed Mn(III)) could partly diffuse into the overlying waters and, together with the estuarine Mn loads carried by the surface waters, transfer large amounts of reactive Mn into open coastal areas and subsequently contribute to Mn shuttling and inter-linked biogeochemical processes over the seafloor. Given the widespread occurrence of acid sulfate soils and other sulfidic geological materials on many coastal plains worldwide, the identified Mn attenuation and transport mechanisms are relevant for many estuaries globally.