This study elucidates how riverbank filtration alters hyporheic zone hydrodynamics and redox conditions to drive Fe²⁺/Mn²⁺ transformations via microbial processes. It aims to quantify the spatial heterogeneity of Fe²⁺/Mn²⁺ cycling microbial metabolism and metal migration in the riverside filtration system; then, a three-layer redox gradient model and repair strategy with engineering applicability are established. The purpose is to provide a theoretical basis for microbial regulation to reduce heavy metal pollution. Multi-omics analyses (16S rRNA sequencing, hydrogeochemistry, metagenomics) in the Liaohe River revealed, in shallow zones (0-17 m), Proteobacteria (38.7%) and iron-reducers (Geobacter) correlated with Fe²⁺ (R² = 0.83), indicating dissimilatory iron reduction dominates iron mobilization. In deep zones (17-350 m), sulfate-reducers (Desulfobacca) generated S²⁻ to precipitate Mn²⁺/Fe²⁺ (removal: 40-60%). A novel three-tier microbial redox-driven zonation model delineated O₂/NO₃⁻-reducing (0-5 m), Fe³⁺/Mn⁴⁺-reducing (5-17 m), and SO₄²⁻-reducing zones (17-350 m) with 85% prediction accuracy at the same latitude. Field implementations reduced treatment costs versus chemical methods, proving scalability for developing regions.