Acid mine drainage (AMD) raises a global environmental concern impacting the iron cycle. Although the formation of Fe(III) minerals in AMD-impacted waters has previously been reported to be regulated by biological processes, the role of abiotic processes remains largely unknown. This study first reported that a photochemical reaction coupled with O₂ significantly accelerated the formation of Fe(III) flocculates (i.e., schwertmannite) in the AMD, as evidenced by the comparison of samples from contaminated sites across different natural conditions at latitudes 24–29° N. Combined with experimental and modeling results, it is further discovered that the intramolecular oxidation of photogenerated Fe(II) with a five-coordinative pyramidal configuration (i.e., [(H₂O)₅Fe]²⁺) by O₂ was the key in enhancing the photooxidation of Fe(II) in the simulated AMD. The in situ attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR), UV–vis spectroscopy, solvent substitution, and quantum yield analyses indicated that, acting as a precursor for flocculation, [(H₂O)₅Fe]²⁺ likely originated from both the dissolved and colloidal forms of Fe(III) through homogeneous and surface ligand-to-metal charge transfers. Density functional theory calculations and X-ray absorption spectroscopy results further suggested that the specific oxidation pathways of Fe(II) produced the highly reactive iron species and triggered the hydrolysis and formation of transient dihydroxo dimers. The proposed new pathways of Fe cycle are crucial in controlling the mobility of heavy metal anions in acidic waters and enhance the understanding of complicated iron biochemistry that is related to the fate of contaminants and nutrients.