Biochars can remove potentially toxic elements, such as inorganic mercury [Hg(II)] from contaminated waters. However, their performance in complex water matrices is rarely investigated, and the combined roles of natural organic matter (NOM) and ionic composition in the removal of Hg(II) by biochar remain unclear. Here, we investigate the influence of NOM and major ions such as chloride (Cl–), nitrate (NO3–), calcium (Ca2+), and sodium (Na+) on Hg(II) removal by a wood-based biochar (SWP700). Multiple sorption sites containing sulfur (S) were located within the porous SWP700. In the absence of NOM, Hg(II) removal was driven by these sites. Ca2+ bridging was important in enhancing removal of negatively charged Hg(II)-chloro complexes. In the presence of NOM, formation of soluble Hg-NOM complexes (as seen from speciation calculations), which have limited access to biochar pores, suppressed Hg(II) removal, but Cl– and Ca2+ could still facilitate it. The ability of Ca2+ to aggregate NOM, including Hg-NOM complexes, promoted Hg(II) removal from the dissolved fraction (<0.45 μm). Hg(II) removal in the presence of Cl– followed a stepwise mechanism. Weakly bound oxygen functional groups in NOM were outcompeted by Cl–, forming smaller-sized Hg(II)-chloro complexes, which could access additional intraparticle sorption sites. Therein, Cl– was outcompeted by S, which finally immobilized Hg(II) in SWP700 as confirmed by extended X-ray absorption fine structure spectroscopy. We conclude that in NOM containing oxic waters, with relatively high molar ratios of Cl–: NOM and Ca2+: NOM, Hg(II) removal can still be effective with SWP700.