Bioremediation of acid mine drainage (AMD) was often challenged by poor tolerance of sulfate-reducing bacteria (SRB) to heavy metals and low bioactivity. The highly active immobilized particles with Fe0/Fe2+ enhanced SRB (Fe0/2+-SRB) were prepared by the microorganism immobilization technique. Three dynamic columns were constructed to investigate the adsorption capacity of Fe0/2+-SRB for Mn2+ under varying adsorption layer heights, inflow velocity, and initial Mn2+ concentrations. The role of each matrix material in the immobilized particles was explored, the mechanism of AMD remediation by Fe0/2+-SRB was revealed, and the adaptability of Fe0/2+-SRB to AMD under various initial conditions was investigated. The results showed that the prepared Fe0/2+-SRB exhibited a well-developed surface pore structure. When the adsorption layer height was 200 mm, the influent flow rate was 5 × 10−5 m3/s, and the initial manganese ion concentration was 10 mg/L, the maximum dynamic adsorption capacities (qe) of Mn2+ for each dynamic column were 7.8430, 4.7627, and 8.7677 mg/g, respectively. Compared to dynamic columns 1# and 2#, dynamic column 3# showed the best performance in treating AMD, and the Thomas model effectively described the adsorption kinetics of Mn2+ by Fe0/2+-SRB(3#). Microstructural analysis indicated that chemical adsorption, ion exchange, dissimilation–reduction reaction, and surface complexation occurred between the various matrix materials in Fe0/2+-SRB(3#). Mn2+ was primarily removed in the form of metal sulfide (MnS), and Fe0/Fe2+ could promote the dissimilatory reduction of SO42− by SRB to form S2−. Fe0/2+-SRB(3#) was able to adapt to AMD with initial conditions of pH was 2~4, SO42− < 2500 mg/L, and Mn2+ < 20 mg/L. The research results provide new insights into the remediation of AMD, using a combined microbial-adsorption technology.