Abstract: Iron and manganese ions are the primary characteristic pollutants in acid mine water (AMD) and present key challenges in the treatment of contaminated mine groundwater. This study constructed a laboratory-scale limestone neutralization–vertical flow reactor system to treat AMD characterized by low pH, high iron concentrations, and elevated manganese levels. The treatment effects of series system on AMD under different conditions such as iron and manganese concentrations, hydraulic retention time, and initial pH, were investigated. The results show that the removal rate of iron (Fe²⁺, TFe) in the series system can reach 99%, and the total iron concentration in the effluent can be reduced to less than 0.1 mg/L, while the removal rate of manganese (Mn²⁺) can reach 97%, with the effluent concentration less than 0.2 mg/L. Compared with the single treatment system, the concentrations of iron and manganese in the effluent were significantly reduced. XRD analysis showed that the main products of the neutralization process were goethite and iron hydroxide, and the main products in the vertical flow reactor were goethite and manganese oxide. XPS and SEM analysis indicated that heterogeneous catalytic oxidation and adsorption were the primary mechanisms driving further removal of iron and manganese. This study presents that the limestone neutralization-vertical flow reactor series system is an effective method for treating AMD with low acidity, high iron, and low manganese mine water, providing a new technical approach for mine water remediation.