The Madeira is one of the major tributaries of the Amazon River and is characterized by a large alluvial floodplain throughout the stream continuum. This study aims to better assess the hydrological functioning of the Madeira Basin over its alluvial floodplains at both local and global scales. We used the semi-distributed hydrological Soil and Water Assessment Tool (SWAT) model to simulate water discharge at a daily time step and water resources for each hydrological compartment. A new hydraulic module for water routing was implemented in the SWAT model considering the floodplain either as a simple reservoir or as a continuum where the water can flow along with the floodplain network. Both water surface estimated by L-band passive microwaves (SWAF data) and digital elevation model—shuttle radar topography mission (DEM–SRTM data) were used to delineate the floodplain, as inputs for the model. On the global scale, the amount of water stored in the Madeira floodplain is between 810 ± 230 km 3 per year when the floodplains are delimited with SWAF and 1,300 ± 350 km 3 per year with the DEM floodplain delineation between 2008 and 2018. Spatial altimetry (Jason 2-3) data were also applied to alluvial areas to validate the water height dynamic in floodplains at a local scale. Results show that more than 60% of the alluvial validation points display a correlation above 0.40 ± 0.02 regardless of the floodplain delineation. This study permits us to better characterize the spatio-temporal storage dynamics of the Madeira floodplains at both local and global scales, and it underlines the importance of a precise floodplain delineation, before computing biogeochemical fluxes and sediment yield.