In this study we used satellite altimetry to characterize the time and space variations in water stored in or circulating through rivers, floodplains, wetlands and lakes in the major sub-basins of the Amazon basin. Using a specific methodology to rigorously select original three-dimensional (3D) data from an Environmental Satellite (ENVISAT) mission, water level time series were calculated at the crossing path of the satellite tracks with the water bodies. We took advantage of the continuous sampling of the water level along the satellite track segments that cross the watershed to analyse both spatial and temporal relationships between: (i) the river and its floodplain and (ii) different basins. This work evidences in particular the existence of water leaking between the Negro and Solimões basins at the high water stage. It highlights that the phenomenon of a secondary flood peak occurring in the water level series in the Solimões basin at rising water, known as repiquete, is caused by the rain equatorial regime of the northern upstream tributaries of the Solimões River, but is disconnected from the same phenomenon occurring within the Rio Negro basin.