Although subsurface horizons store more than half the total soil organic carbon (SOC) globally, the sources and dynamics of subsurface SOC are still unknown. Root litter input and dissolved organic carbon (DOC) transport are possible sources. Using a vertically extended soil C model, we explore the role of root C input and DOC transport in controlling subsurface SOC dynamics. The model involves organic matter decomposition and DOC leaching in the aboveground litter layer, the belowground input of C from roots, and SOC turnover and DOC transport along water flows throughout the soil profile for three SOC pools (active, slow, and passive — characterized by a turnover time of years, decades, and millennia, respectively). Model simulations with a range of rooting profiles demonstrate that a large proportion (36% – 78% — greater in deeper rooting profiles) of SOC is apportioned to the subsurface horizons (below the top 30 cm). A significant part (39% – 73%) of subsurface SOC was found to be associated with C pools that turn over on time scales of decades or less. DOC transport appeared to be dominant in distributing the added C to the deeper soil layers, making the SOC content profile deeper than that of the root litter (C) input. The results suggest that current soil C studies focusing on the surface alone, significantly underestimate the stock of decadally cycling C, especially for deeply rooted ecosystems. Studies ignoring subsurface C dynamics therefore underpredict the responses of soil C to changes in climate, land use, and vegetation.