Riverbed scouring and siltation, affected by variations in river flow and sediment concentration, can cause changes in the sediment thickness, leading to the complex feedback between riverbed permeability and nutrient–reactive transport processes. Currently, the migration and transformation of iron and manganese under changed riverbed sediment thickness have not been taken into account. Based on indoor one-dimensional soil column simulation experiments, along with in-situ monitoring, Rhizon pore water sampling, and 16 s rRNA high-throughput sequencing technologies, this study revealed the migration and transformation patterns of iron and manganese in the river infiltration zone and their contribution rates under different sediment thickness conditions. The results demonstrated that as the riverbed sediment thickness increased, the river infiltration rate and sediment permeability coefficient demonstrated a significant decrease over time. For instance, a 5 cm sediment thickness can decrease the sediment permeability coefficient by 30 % within 32 d of infiltration, expand the disconnection zone to 25 cm, narrow the oxidation–reduction zone, and cause the iron and manganese reduction zone to evolve from a single peak to a double peak pattern. Additionally, as the sediment thickness increased, the contribution of organic matter bound iron-manganese oxidation and iron-manganese oxide reduction to Mn2+ and Fe2+ concentrations in sediment pore water decreased, while the contribution of adsorption and complexation-precipitation increased. This study holds great significance for ensuring the safety of drinking water supply and promoting the sustainable utilization of groundwater resources.