The chemical speciation of mercury (Hg), methyl mercury (MeHg), sulfur and iron was investigated in the sediment and porewater of Lake Ängessjön, a boreal, shallow (maximum depth 2.5 m), oligo-/dystrophic lake in northern Sweden. The lake receives terrestrial stream runoff from surrounding coniferous forest soils and peatlands having a low pH (4.6) and high concentrations of dissolved organic matter (DOM, annual average: 45 mg L−1), Fe (60 µM), sulfate (105 µM), inorganic Hg (1200 pM) and MeHg (250 pM). Sulfur K-edge XANES and Hg LIII-edge EXAFS spectroscopic measurements were used to characterize and quantify the sulfur speciation in the lake sediment at nine occasions, covering different seasons in the years of 2007 and 2009. In the surface sediment (0–3 cm) sulfate is reduced to zero-valent S and inorganic sulfide, that in turn reacts with Fe to form FeSm (mackinawite) and FeS2 (framboidal pyrite). The latter mineral becomes increasingly dominant by depth in the sediment. Thermodynamic modeling successfully predicted measured porewater concentrations of Hg in the sediment. Metacinnabar (β-HgS) and Hg(NOM-RS)2 complexes (the latter formed as a reaction between Hg(II) and thiol groups associated with natural organic matter, NOM-RSH) were the dominant forms of Hg(II) in the solid phase of sediments and Hg(II)-polysulfides (aq) dominated in the porewater. We argue that FeSm is a key component that indirectly controlled the Hg(II) speciation in the sediment by keeping the aqueous phase concentration of inorganic sulfide in the 0.5–2 µM range throughout the year. Besides providing a pool of readily soluble inorganic sulfide for formation of β-HgS(s), as demonstrated by previously reported EXAFS experiments, we further suggest FeSm may serve as a precursor for the formation of a more crystalline (less soluble) β-HgS(s) phase than present in environments devoid of FeSm. Support for this was provided by comparing our results with previously reported thermodynamic modelling results of Hg(II) and MeHg solubility in organic soils devoid of FeSm. In more general terms, we suggest the presence or absence of FeSm, through its influence on the chemical speciation of Hg and MeHg, may be a key factor behind the variability in rates of Hg(II) and MeHg transformation processes, such as methylation, reduction and demethylation, reported for different environmental settings.