Many surface soils are enriched in metals due to anthropogenic atmospheric inputs. To predict the persistence of these contaminants in soils, factors that impact rates of metal removal from soils into streams must be understood. Experiments at containerized seedling (mesocosm), pedon, and catchment scales were used to investigate the influence of vegetation on manganese (Mn) transport at the Susquehanna/Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA, where past atmospheric inputs from industrial sources have enriched Mn in surface soils. Large quantities of Mn that were leached from soil components into solution were taken up by vegetation; as a result, only relatively small quantities of Mn were removed from soil into effluent and streams. Manganese uptake into vegetation exceeded Mn losses in soil leachate by 20–200X at all scales, and net Mn loss from soils decreased in the presence of vegetation due to uptake into plant tissues. The majority of Mn taken up by forest vegetation at SSHCZO each year was returned to the soil in leaf litter and consequently immobilized as Mn oxides that formed during litter decomposition. Thus, plant uptake of Mn combined with rapid oxidation of Mn during litter decomposition contribute to long-term retention. Current release rates of soluble Mn from SSHCZO soils were similar to release rates from the larger Susquehanna River Basin, indicating that the processes observed at SSHCZO may be widespread across the region. Indeed, although atmospheric deposition of Mn has declined, surface soils at SSHCZO and throughout the eastern United States remain enriched in Mn. If recycling through vegetation can attenuate the removal of Mn from soils, as observed in this study, then Mn concentrations in soils and river waters will likely decrease slowly over time following watershed contamination. Understanding the role of vegetation in regulating metal transport is important for evaluating the long-term effects of historical and ongoing metal loading to soils.