In sediments, manganese (Mn) is typically enriched in the form of authigenic Mn hydroxides at the water-sediment interface where intensive redox cycling of Mn occurs. Here we show, based on existing hydrochemical and geochemical (sediment core) data and new detailed chemical and mineralogical characterization of a 3.5 m long sediment core from a Boreal estuary, that the behavior of Mn can be profoundly different and more complex in estuarine settings receiving an abundance of terrestrial Mn. The most notable feature in the 3.5 m long sediment core is two depth intervals (60–155 cm and 181–230 cm) where there are strong fine-scale variations in Mn concentrations with peaks episodically reaching up to 10–25 g kg− 1 and 6.7–12 g kg− 1, respectively. X-ray absorption spectroscopy and sequential chemical extraction show that Mn occurs mainly as authigenic rhodochrosite at these two depth intervals and is mainly surface-sorbed in other sections with relatively low and stable Mn concentrations. The data suggests that the strong fine-scale variations in Mn concentrations are a reflection of the extent of formation and settling of Mn hydroxides, the precursors of the authigenic rhodochrosite (and also of the surface-sorbed Mn), rather than Mn input to the estuary or redox-related Mn translocation within the sediment. There was agreement between the results of linear combination fitting of extended X-ray absorption fine structure data and a 7-step sequential chemical extraction (SCE) in terms of quantification of surface-sorbed Mn species, whereas the SCE experiment failed to fractionate a majority of rhodochrosite into SCE step-2 (1 M NH4-acetate at pH 6), which is frequently employed to dissolve carbonate. We ascribe this discrepancy to only partial dissolution of rhodochrosite in the weakly acidic (pH = 6) NH4-acetate leach.