A natural wetland that has historically received acid mine drainage (AMD) from the abandoned metal mine at Parys Mountain (Anglesey, UK) has proved efficient in the removal of Fe and other trace metals. This study aims to evaluate the microbial and physicochemical mechanisms involved in the metal attenuation process observed along the wetland by assessing the role of the microbial communities and microbial-derived changes in metal chemistry that leads to an improvement in the water quality. A combination of molecular microbiology approaches, metal analytical techniques and microcosm experiments show that the wetland retains the diversity and metabolic structure of sediment bacteria communities despite the high acidity and metal concentration. In the middle of the wetland, increased bacterial activity related to Fe and S oxidation coincided with a removal of sulphate and metals from the water column. Incubation experiments of wetland sediments showed that the presence of bacteria generated higher levels of sulphide and particulate metals in the water column and the abundance of metabolic pathways related to AMD remediation was influenced by organic matter through increase in bacterial sulphate reduction activity. The findings of this study suggest that sediment bacteria are a key component that contributes to the immobilisation of Fe and trace metals observed in adapted natural wetlands to AMD pollution.