The presence of manganese(II) in drinking water sources poses a significant treatment difficulty for water utilities, thus necessitating the development of effective removal strategies. Treatment by Fe(VI), a combined oxidant and coagulant, has been identified as a potential green solution; however, its effectiveness is hampered by natural organic matter (NOM), and this underlying mechanism is not fully understood. Here, we investigated the inhibitory effect of three different types of NOM, representing terrestrial, aquatic, and microbial origins, on Mn(II) removal and floc growth during Fe(VI) coagulation. Results revealed that Fe(VI) coagulation effectively removes Mn(II), but NOM could inhibit its effectiveness by competing in oxidation reactions, forming NOM-Fe complexes, and altering floc aggregation. Humic acid was found to exhibit the strongest inhibition due to its unsaturated heterocyclic species that strongly bond to flocs and react with Fe(VI). For the first time, this study has presented a comprehensive elucidation of the atomic-level structure of Fe(VI) hydrolysis products by employing Extended X-ray Absorption Fine Structure Spectroscopy (EXAFS). Results demonstrated that NOM strengthened single-corner and double-corner coordination between FeO6 octahedrons that were consumed by Mn(II), resulting in an increased contribution of γ-FeOOH in the core-shell structure (γ-FeOOH shell and γ-F2O3 core), thereby inhibiting coagulation effects. Furthermore, NOM impeded the formation of stable manganite, resulting in more low-valence Mn(III) being incorporated in the form of an unstable intermediate. These findings provide a deeper understanding of the complex interplay between Fe coagulants, heavy metal pollution, and NOM in water treatment and offer insight into the limitations of Fe(VI) in practical applications.