Ferric hydroxide precipitation and flocculation is the most commonly used method for the removal of arsenic in water treatment. However, citrate often interrupts the precipitation of ferric hydroxides and thus affects arsenic removal. To date, the mechanisms controlling the effects of citrate on arsenic removal with ferric hydroxide flocculation and precipitation at very low citrate-to-Fe molar ratios are not well understood. Herein, we report a new mechanism by which citrate inhibits arsenic removal using ferric hydroxide. At a substoichiometric citrate-to-Fe molar ratio of 0.28, citrate forms a high-molecular-weight Fe−citrate (Fe Cit) species. The optimized structure of the Fe Cit species was obtained by the density functional theory calculation. To the best of our knowledge, this study is the first to report the formation and to identify the structure of dominant Fe–citrate species at a very low citrate-to-Fe molar ratio.