In the Congo River Basin (CRB), due to the lack of contemporary in situ observations, there is a limited understanding of the large-scale variability of its present-day hydrologic components and their link with climate. In this context, remote sensing observations provide a unique opportunity to better characterize those dynamics. Analyzing the Global Inundation Extent Multi-Satellite (GIEMS) time series, we first show that surface water extent (SWE) exhibits marked seasonal patterns, well distributed along the major rivers and their tributaries, and with two annual maxima located: i) in the lakes region of the Lwalaba sub-basin and ii) in the “Cuvette Centrale”, including Tumba and Mai-Ndombe Lakes. At an interannual time scale, we show that SWE variability is influenced by ENSO and the Indian Ocean dipole events. We then estimate water level maps and surface water storage (SWS) in floodplains, lakes, rivers and wetlands of the CRB, over the period 2003-2007, using a multi-satellite approach, which combines the GIEMS dataset with the water level measurements derived from the ENVISAT altimeter heights. The mean annual variation in SWS in the CRB is 81±24 km3 and contributes to 19±5 % of the annual variations of GRACE-derived terrestrial water storage (33±7 % in the Middle Congo). It represents also ~6±2 % of the annual water volume that flows from the Congo River into the Atlantic Ocean.