Observational studies across the Amazon report a common occurrence of shallow water table in lowland valleys and groundwater-surface water exchange from small headwater catchments to large floodplains. In this study, we assess groundwater's role in the Amazon surface water dynamics using a continental-scale coupled groundwater-surface water model (LEAF-Hydro-Flood) forced by ERA-Interim reanalysis, at 2 km and 4 min resolution over 11 years (2000–2010). The simulation is validated with observed streamflow, water table depth and flooding extent. A parallel simulation without groundwater is conducted to isolate its effect. Our findings support the following hypotheses. First, in the headwater catchments, groundwater dominates streamflow; the observed variations in its dominance across the Amazon can be explained by the varying water table depth. Second, over large floodplains, there are two-way exchanges between floodwater and groundwater as infiltration in the wet season and seepage in the dry season, and the direction and magnitude are controlled by the water table depth. Third, the Amazon harbors large areas of wetlands that are rarely under floodwater and difficult to observe by remote sensing, but are maintained by a persistently shallow water table. Fourth, due to its delayed and muted response to rainfall, groundwater seepage persists in the dry season, buffering surface waters through seasonal droughts. Our simulations shed new lights on the spatial-temporal structures of the hidden subsurface hydrologic pathways across the Amazon and suggest possible mechanisms whereby groundwater actively participates in the Amazon water-carbon cycle such as CO2 outgassing from groundwater seeps and CH4 emission from groundwater-supported wetlands.